Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold480
Parameters: 2 7 7 80 10 50 1000
Pmatch=0.80,Pindel=0.10
tuple sizes 0,4,5,7
tuple distances 0, 29, 159, 1000
Length: 956445
ACGTcount: A:0.33, C:0.16, G:0.17, T:0.34
File 3 of 7
Found at i:294581 original size:176 final size:176
Alignment explanation
Indices: 294271--295046 Score: 895
Period size: 176 Copynumber: 4.4 Consensus size: 176
294261 ACTTTTTAGC
* * * *
294271 CCTCAAAAAGCAGGATGCCTTTTCCTTTTAAAACCCACACAAGTTGGCGGCACC-TTCAGTCCTC
1 CCTCAAAGAGCAGGACGCCTTTT-CTTTTAAAGCCCACACAAGTTGGTGGCACCTTTCAGTCCTC
* * *
294335 AAAGAGCAGGACACCTTTTAAAGCCCTCACAAGTTGGTGGCA-CTTCCCAGTCCTCAAAAAGCAG
65 AAAGAGCAGGACCCCTTTTAAAG-CCACACAAGTTGGTGGCACCTTCCCAGTCCTCAAAGAGCAG
* * *
294399 GACGCCTTCTCCTTTCAAAGCCCATACAAGTTGGTGGCATTTTCCAGT
129 GACGCCTTCTCCTTTTAAAGCCCACACAAGTTGGTGGCACTTTCCAGT
* * * *
294447 CCTTAAAGAGCGGGACGCCTTTTCTTTCAAAGCCCACACAAGTTGGTGGCACCTTTTC-GTCCCC
1 CCTCAAAGAGCAGGACGCCTTTTCTTTTAAAGCCCACACAAGTTGGTGGCACC-TTTCAGTCCTC
294511 AAAGAGCAGGACCCCTTTTAAAGCCAACACAAGTTGGTGGCA-CTTCCCAGTCCTCAAAGAGCAG
65 AAAGAGCAGGACCCCTTTTAAAGCC-ACACAAGTTGGTGGCACCTTCCCAGTCCTCAAAGAGCAG
* *
294575 GACGCCTTCTCCTTTTAAAGCCCACACAAGTTGGTGGCATTTTCTAGT
129 GACGCCTTCTCCTTTTAAAGCCCACACAAGTTGGTGGCACTTTCCAGT
* * * * *
294623 CCTCAAAAAGCGGGACACCTTTTCTTTTAAAGCCCACACAAATTGGTGGCACC-TCCAGTCCTCA
1 CCTCAAAGAGCAGGACGCCTTTTCTTTTAAAGCCCACACAAGTTGGTGGCACCTTTCAGTCCTCA
* * * *
294687 AAGAGCGGGACACCTTTTCTTTCAAAGCTCACACAAGTTGGTGGCACCTTTCC-GTCCCCAAAGA
66 AAGAGCAGGAC-CC----CTTTTAAAGC-CACACAAGTTGGTGGCACCTTCCCAGTCCTCAAAGA
* *
294751 GTAGGA---C--C-CCTTTTAAAGCCCACACAAGTTGGTGGCACTTCCCAGT
125 GCAGGACGCCTTCTCCTTTTAAAGCCCACACAAGTTGGTGGCACTTTCCAGT
* * * *
294797 CCTCAAAGAGCAGGATGCCTTCTCCTTTTAAAGCCGACACAAGTTGGTGGCA-TTTTCCAGTCCT
1 CCTCAAAGAGCAGGACGCCTT-TTCTTTTAAAGCCCACACAAGTTGGTGGCACCTTT-CAGTCCT
* *
294861 CAAAGAGCGGGATGCCTTTTCTTTTAAAGCCTACACAAGTTGGTGGCACCTT--CAGTCCTCAAA
64 CAAAGAGCAGGA--CC---CCTTTTAAAGCC-ACACAAGTTGGTGGCACCTTCCCAGTCCTCAAA
* * *
294924 GAGCGGGACGCCTT-TTCTTTTAAAGCCCAC-CTAAGTTGGTGGCACCTT-CAGT
123 GAGCAGGACGCCTTCTCCTTTTAAAGCCCACAC-AAGTTGGTGGCACTTTCCAGT
* * *
294976 CCTCAAAGAGCAGGATGCTTTTTCTTTTCAAAGCCCACACAAGTTGGTGGCACCTTTCAGTCCCC
1 CCTCAAAGAGCAGGACGCCTTTTCTTTT-AAAGCCCACACAAGTTGGTGGCACCTTTCAGTCCTC
295041 AAAGAG
65 AAAGAG
295047 TGTTAAGTCG
Statistics
Matches: 519, Mismatches: 51, Indels: 57
0.83 0.08 0.09
Matches are distributed among these distances:
174 55 0.11
175 89 0.17
176 225 0.43
177 5 0.01
178 8 0.02
179 60 0.12
180 71 0.14
181 6 0.01
ACGTcount: A:0.26, C:0.29, G:0.20, T:0.25
Consensus pattern (176 bp):
CCTCAAAGAGCAGGACGCCTTTTCTTTTAAAGCCCACACAAGTTGGTGGCACCTTTCAGTCCTCA
AAGAGCAGGACCCCTTTTAAAGCCACACAAGTTGGTGGCACCTTCCCAGTCCTCAAAGAGCAGGA
CGCCTTCTCCTTTTAAAGCCCACACAAGTTGGTGGCACTTTCCAGT
Found at i:294722 original size:235 final size:234
Alignment explanation
Indices: 294294--295046 Score: 1015
Period size: 235 Copynumber: 3.2 Consensus size: 234
294284 GATGCCTTTT
* * *
294294 CCTTTTAAAACCCACACAAGTTGGCGGCACCTT--CAGTCCTCAAAGAGCAGGA-----CACCTT
1 CCTTTTAAAGCCCACACAAGTTGGTGGCA-CTTCCCAGTCCTCAAAGAGCAGGAGCCTTCTCCTT
* * * * * *
294352 TTAAAGCCCTCACAAGTTGGTGGCACTTCCCAGTCCTCAAAAAGCAGGACGCCTTCTCCTTTCAA
65 TTAAAGCCCACACAAGTTGGTGGCATTTTCCAGTCCTCAAAAAGCGGGACGCCTT-TTCTTTTAA
* ** *
294417 AGCCCATACAAGTTGGTGGCATTTTCCAGTCCTTAAAGAGCGGGACGCCTTTTCTTTCAAAGCCC
129 AGCCCACACAAGTTGGTGGCA-CCTCCAGTCCTCAAAGAGCGGGACGCCTTTTCTTTCAAAGCCC
294482 ACACAAGTTGGTGGCACCTTTTCGTCCCCAAAGAGCAGGACC
193 ACACAAGTTGGTGGCACCTTTTCGTCCCCAAAGAGCAGGACC
*
294524 CCTTTTAAAGCCAACACAAGTTGGTGGCACTTCCCAGTCCTCAAAGAGCAGGACGCCTTCTCCTT
1 CCTTTTAAAGCCCACACAAGTTGGTGGCACTTCCCAGTCCTCAAAGAGCAGGA-GCCTTCTCCTT
* *
294589 TTAAAGCCCACACAAGTTGGTGGCATTTTCTAGTCCTCAAAAAGCGGGACACCTTTTCTTTTAAA
65 TTAAAGCCCACACAAGTTGGTGGCATTTTCCAGTCCTCAAAAAGCGGGACGCCTTTTCTTTTAAA
* * *
294654 GCCCACACAAATTGGTGGCACCTCCAGTCCTCAAAGAGCGGGACACCTTTTCTTTCAAAGCTCAC
130 GCCCACACAAGTTGGTGGCACCTCCAGTCCTCAAAGAGCGGGACGCCTTTTCTTTCAAAGCCCAC
* *
294719 ACAAGTTGGTGGCACCTTTCCGTCCCCAAAGAGTAGGACC
195 ACAAGTTGGTGGCACCTTTTCGTCCCCAAAGAGCAGGACC
294759 CCTTTTAAAGCCCACACAAGTTGGTGGCACTTCCCAGTCCTCAAAGAGCAGGATGCCTTCTCCTT
1 CCTTTTAAAGCCCACACAAGTTGGTGGCACTTCCCAGTCCTCAAAGAGCAGGA-GCCTTCTCCTT
* * *
294824 TTAAAGCCGACACAAGTTGGTGGCATTTTCCAGTCCTCAAAGAGCGGGATGCCTTTTCTTTTAAA
65 TTAAAGCCCACACAAGTTGGTGGCATTTTCCAGTCCTCAAAAAGCGGGACGCCTTTTCTTTTAAA
* * *
294889 GCCTACACAAGTTGGTGGCACCTTCAGTCCTCAAAGAGCGGGACGCCTTTTCTTTTAAAGCCCAC
130 GCCCACACAAGTTGGTGGCACCTCCAGTCCTCAAAGAGCGGGACGCCTTTTCTTTCAAAGCCCAC
* *
294954 -CTAAGTTGGTGGCACC--TTCAGTCCTCAAAGAGCAGGATGCTTTT
195 AC-AAGTTGGTGGCACCTTTTC-GTCCCCAAAGAGCAGGA--C---C
* * *
294998 TCTTTTCAAAGCCCACACAAGTTGGTGGCACCTT-TCAGTCCCCAAAGAG
1 CCTTTT-AAAGCCCACACAAGTTGGTGGCA-CTTCCCAGTCCTCAAAGAG
295047 TGTTAAGTCG
Statistics
Matches: 465, Mismatches: 41, Indels: 24
0.88 0.08 0.05
Matches are distributed among these distances:
229 3 0.01
230 26 0.06
231 19 0.04
233 2 0.00
234 16 0.03
235 274 0.59
236 27 0.06
237 54 0.12
239 5 0.01
240 36 0.08
241 3 0.01
ACGTcount: A:0.25, C:0.29, G:0.20, T:0.25
Consensus pattern (234 bp):
CCTTTTAAAGCCCACACAAGTTGGTGGCACTTCCCAGTCCTCAAAGAGCAGGAGCCTTCTCCTTT
TAAAGCCCACACAAGTTGGTGGCATTTTCCAGTCCTCAAAAAGCGGGACGCCTTTTCTTTTAAAG
CCCACACAAGTTGGTGGCACCTCCAGTCCTCAAAGAGCGGGACGCCTTTTCTTTCAAAGCCCACA
CAAGTTGGTGGCACCTTTTCGTCCCCAAAGAGCAGGACC
Found at i:295137 original size:21 final size:21
Alignment explanation
Indices: 295111--295168 Score: 107
Period size: 21 Copynumber: 2.8 Consensus size: 21
295101 AAATTATCCA
295111 AATGTATCGATACATTTGTAG
1 AATGTATCGATACATTTGTAG
*
295132 AATGTATCGATACATTTGTGG
1 AATGTATCGATACATTTGTAG
295153 AATGTATCGATACATT
1 AATGTATCGATACATT
295169 CTACAAATGT
Statistics
Matches: 36, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
21 36 1.00
ACGTcount: A:0.33, C:0.10, G:0.19, T:0.38
Consensus pattern (21 bp):
AATGTATCGATACATTTGTAG
Found at i:295177 original size:21 final size:20
Alignment explanation
Indices: 295109--295183 Score: 78
Period size: 21 Copynumber: 3.6 Consensus size: 20
295099 AAAAATTATC
*
295109 CAAATGTATCGATACATTTG
1 CAAATGTATCGATACATTTA
* *
295129 TAGAATGTATCGATACATTTGT
1 CA-AATGTATCGATACATTT-A
**
295151 GGAATGTATCGATACATTCTA
1 CAAATGTATCGATACATT-TA
295172 CAAATGTATCGA
1 CAAATGTATCGA
295184 AGGGTCCCAA
Statistics
Matches: 45, Mismatches: 7, Indels: 5
0.79 0.12 0.09
Matches are distributed among these distances:
20 1 0.02
21 43 0.96
22 1 0.02
ACGTcount: A:0.35, C:0.13, G:0.17, T:0.35
Consensus pattern (20 bp):
CAAATGTATCGATACATTTA
Found at i:295245 original size:19 final size:18
Alignment explanation
Indices: 295219--295318 Score: 71
Period size: 19 Copynumber: 6.0 Consensus size: 18
295209 AATTTCAGCG
295219 ATTTGTATCGATACATAA
1 ATTTGTATCGATACATAA
295237 ATGTTGTATCGATAC---A
1 AT-TTGTATCGATACATAA
295253 A--TGTATCGATACATAA
1 ATTTGTATCGATACATAA
*
295269 GTATTGTATCGATAC---A
1 AT-TTGTATCGATACATAA
295285 A--T-TATCGATACA-AA
1 ATTTGTATCGATACATAA
295299 AGTATTGTATCGATACATAA
1 A-T-TTGTATCGATACATAA
295319 TTAGCTACTG
Statistics
Matches: 65, Mismatches: 2, Indels: 28
0.68 0.02 0.29
Matches are distributed among these distances:
12 9 0.14
13 12 0.18
14 2 0.03
16 4 0.06
18 3 0.05
19 33 0.51
20 2 0.03
ACGTcount: A:0.39, C:0.12, G:0.14, T:0.35
Consensus pattern (18 bp):
ATTTGTATCGATACATAA
Found at i:295294 original size:31 final size:32
Alignment explanation
Indices: 295222--295315 Score: 154
Period size: 32 Copynumber: 3.0 Consensus size: 32
295212 TTCAGCGATT
* *
295222 TGTATCGATACATAAATGTTGTATCGATACAA
1 TGTATCGATACATAAGTATTGTATCGATACAA
295254 TGTATCGATACATAAGTATTGTATCGATACAA
1 TGTATCGATACATAAGTATTGTATCGATACAA
*
295286 T-TATCGATACAAAAGTATTGTATCGATACA
1 TGTATCGATACATAAGTATTGTATCGATACA
295316 TAATTAGCTA
Statistics
Matches: 59, Mismatches: 3, Indels: 1
0.94 0.05 0.02
Matches are distributed among these distances:
31 28 0.47
32 31 0.53
ACGTcount: A:0.38, C:0.13, G:0.15, T:0.34
Consensus pattern (32 bp):
TGTATCGATACATAAGTATTGTATCGATACAA
Found at i:295382 original size:21 final size:21
Alignment explanation
Indices: 295338--295394 Score: 89
Period size: 21 Copynumber: 2.8 Consensus size: 21
295328 GCCAAGGGAA
*
295338 TGTATCGATACAT-TTTTCTG
1 TGTATCGATACATCTATTCTG
*
295358 TGTATCGATACATCTATTCTT
1 TGTATCGATACATCTATTCTG
295379 TGTATCGATACATCTA
1 TGTATCGATACATCTA
295395 GGAAGTTTAC
Statistics
Matches: 34, Mismatches: 2, Indels: 1
0.92 0.05 0.03
Matches are distributed among these distances:
20 13 0.38
21 21 0.62
ACGTcount: A:0.25, C:0.18, G:0.12, T:0.46
Consensus pattern (21 bp):
TGTATCGATACATCTATTCTG
Found at i:297967 original size:51 final size:51
Alignment explanation
Indices: 297902--298120 Score: 249
Period size: 52 Copynumber: 4.2 Consensus size: 51
297892 TATTTCCGAA
* * *** *
297902 GGGATACTCCAACCCCGACTTTATTTCCAAAATATTGATTTTTCATAATCG
1 GGGATACTCCAACCCCGATTTTATTTCCAAAACACCAATTTTTCACAATCG
* * * *
297953 GGGATACTCCAACCCCGGTTTTATTGCTAAAACACTAATTTTTTCACAATCG
1 GGGATACTCCAACCCCGATTTTATTTCCAAAACACCAA-TTTTTCACAATCG
* * * **
298005 GGGATACTCTAACCCCGATTTTATTTTCAAAACACCAATTTTCCTTTAATCG
1 GGGATACTCCAACCCCGATTTTATTTCCAAAACACCAATTTTTC-ACAATCG
* *
298057 GGGATACTCCAACTCCGATTTTATTTCCAAAAATACCAATTTTTCACAATCG
1 GGGATACTCCAACCCCGATTTTATTTCC-AAAACACCAATTTTTCACAATCG
*
298109 AGGATACTCCAA
1 GGGATACTCCAA
298121 TCTCGTTATT
Statistics
Matches: 140, Mismatches: 25, Indels: 5
0.82 0.15 0.03
Matches are distributed among these distances:
51 36 0.26
52 90 0.64
53 14 0.10
ACGTcount: A:0.31, C:0.25, G:0.11, T:0.33
Consensus pattern (51 bp):
GGGATACTCCAACCCCGATTTTATTTCCAAAACACCAATTTTTCACAATCG
Found at i:298155 original size:28 final size:28
Alignment explanation
Indices: 298105--298186 Score: 78
Period size: 28 Copynumber: 2.9 Consensus size: 28
298095 ATTTTTCACA
* * *
298105 ATCGAGGATACTCCAATCTCGTTATTTC
1 ATCGGGGATACTCCAACCCCGTTATTTC
* *
298133 ATCGGGGATACTGCAACCCCGTTACTTC
1 ATCGGGGATACTCCAACCCCGTTATTTC
*
298161 --CGAGGGAACACTCCAACCCCGTTATT
1 ATCG-GGG-ATACTCCAACCCCGTTATT
298187 ATCTCCAAAA
Statistics
Matches: 44, Mismatches: 8, Indels: 4
0.79 0.14 0.07
Matches are distributed among these distances:
26 2 0.05
27 3 0.07
28 39 0.89
ACGTcount: A:0.24, C:0.30, G:0.18, T:0.27
Consensus pattern (28 bp):
ATCGGGGATACTCCAACCCCGTTATTTC
Found at i:309602 original size:28 final size:28
Alignment explanation
Indices: 309546--309617 Score: 90
Period size: 28 Copynumber: 2.6 Consensus size: 28
309536 AAAATAAAGC
** **
309546 CGGGGTTGGAGTATCCCCTCGGAGGTAA
1 CGGGGTTGGAGTATCCCCGAGGAAATAA
*
309574 CGGGGTTGGAGTATCCCCGATGAAATAA
1 CGGGGTTGGAGTATCCCCGAGGAAATAA
*
309602 CGAGGTTGGAGTATCC
1 CGGGGTTGGAGTATCC
309618 TCAATTGTGA
Statistics
Matches: 38, Mismatches: 6, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
28 38 1.00
ACGTcount: A:0.22, C:0.19, G:0.36, T:0.22
Consensus pattern (28 bp):
CGGGGTTGGAGTATCCCCGAGGAAATAA
Found at i:309602 original size:107 final size:108
Alignment explanation
Indices: 309467--309671 Score: 279
Period size: 107 Copynumber: 1.9 Consensus size: 108
309457 GAAATAAAAT
** * *
309467 CGGGATTGGAGTATCCCCTCGGAAATAACGGGGTTGGAGTATCCCCAATTATG-AGAAATCAAT-
1 CGGGATTGGAGTATCCCCGAGGAAATAACGAGGTTGGAGTATCCCCAATTATGAAAAAAT-AATG
*
309530 ATTTTGAAAATAAAGCCGGGGTTGGAGTATCCCCTCGGAGGTAA
65 ATTTTGAAAATAAAACCGGGGTTGGAGTATCCCCTCGGAGGTAA
* * * * *
309574 CGGGGTTGGAGTATCCCCGATGAAATAACGAGGTTGGAGTATCCTCAATTGTGAAAAAATAATGT
1 CGGGATTGGAGTATCCCCGAGGAAATAACGAGGTTGGAGTATCCCCAATTATGAAAAAATAATGA
* *
309639 TTTTGGAAATAAAATCGGGGTTGGAGTATCCCC
66 TTTTGAAAATAAAACCGGGGTTGGAGTATCCCC
309672 GATTAAAGGA
Statistics
Matches: 84, Mismatches: 12, Indels: 3
0.85 0.12 0.03
Matches are distributed among these distances:
107 49 0.58
108 35 0.42
ACGTcount: A:0.30, C:0.16, G:0.28, T:0.26
Consensus pattern (108 bp):
CGGGATTGGAGTATCCCCGAGGAAATAACGAGGTTGGAGTATCCCCAATTATGAAAAAATAATGA
TTTTGAAAATAAAACCGGGGTTGGAGTATCCCCTCGGAGGTAA
Found at i:309760 original size:50 final size:49
Alignment explanation
Indices: 309605--309823 Score: 208
Period size: 50 Copynumber: 4.3 Consensus size: 49
309595 GAAATAACGA
* * *
309605 GGTTGGAGTATCCTCAATTGTGAAAAAATAATGT-TTTTGGAAATAAAATCGG
1 GGTTGGAGTATCCCCAATTGTG--AAAATTA-GTATTTT-GAAATAAAACCGG
* * *
309657 GGTTGGAGTATCCCCGATTAAAG-GAAAATTGGTGTTTTGAAAATAAAACCGG
1 GGTTGGAGTATCCCCAATT---GTGAAAATTAGTATTTTG-AAATAAAACCGG
*
309709 GGTTGGAGTATCCCCAATTGTGAAAATTAGTATTTTAGAAATAAAATCGG
1 GGTTGGAGTATCCCCAATTGTGAAAATTAGTATTTT-GAAATAAAACCGG
* * * * * *
309759 GGTTTGAGTATCCCCGATTATGAGAAATCAATATTTTGAAATAAAGCCGG
1 GGTTGGAGTATCCCCAATTGTGA-AAATTAGTATTTTGAAATAAAACCGG
*
309809 GGTTAGAGTATCCCC
1 GGTTGGAGTATCCCC
309824 TCGGAGGTAA
Statistics
Matches: 142, Mismatches: 17, Indels: 18
0.80 0.10 0.10
Matches are distributed among these distances:
49 1 0.01
50 69 0.49
51 15 0.11
52 55 0.39
54 1 0.01
55 1 0.01
ACGTcount: A:0.34, C:0.12, G:0.24, T:0.30
Consensus pattern (49 bp):
GGTTGGAGTATCCCCAATTGTGAAAATTAGTATTTTGAAATAAAACCGG
Found at i:309848 original size:260 final size:262
Alignment explanation
Indices: 309495--309997 Score: 859
Period size: 260 Copynumber: 1.9 Consensus size: 262
309485 TCGGAAATAA
*
309495 CGGGGTTGGAGTATCCCCAATTATGAGAAATCAATATTTTGAAAATAAAGCCGGGGTTGGAGTAT
1 CGGGGTTGGAGTATCCCCAATTATGAGAAATCAATATTTTGAAAATAAAGCCGGGGTTAGAGTAT
*
309560 CCCCTCGGAGGTAACGGGGTTGGAGTATCCCCGATGAAATAACGAGGTTGGAGTATCCTCAATTG
66 CCCCTCGGAGGTAACGGGGTTAGAGTATCCCCGATGAAATAACGAGGTTGGAGTATCCTCAATTG
*
309625 TGAAAAAATAATGTTTTTGGAAATAAAATCGGGGTTGGAGTATCCCCGATTAAAGGAAAATTGGT
131 TGAAAAAATAATGTTTTTGGAAATAAAATCGGAGTTGGAGTATCCCCGATTAAAGGAAAATTGGT
*
309690 GTTTT-GAAAATAAAACCGGGGTTGGAGTATCCCCAATTGTGAA-AATTAGTATTTTAGAAATAA
196 GTTTTAG-AAATAAAACCGGGGTTGGAGTATCCCCAATTATGAATAATTAGTATTTTAGAAATAA
309753 AAT
260 AAT
* *
309756 CGGGGTTTGAGTATCCCCGATTATGAGAAATCAATATTTTG-AAATAAAGCCGGGGTTAGAGTAT
1 CGGGGTTGGAGTATCCCCAATTATGAGAAATCAATATTTTGAAAATAAAGCCGGGGTTAGAGTAT
* *
309820 CCCCTCGGAGGTAATGGGGTTAGAGTATCCCCGATGAAATAACGAGGTTGGAGTATCCTCGATTG
66 CCCCTCGGAGGTAACGGGGTTAGAGTATCCCCGATGAAATAACGAGGTTGGAGTATCCTCAATTG
* **
309885 TGAAAAATTGGTGTTTTTGGAAATAAAATCGGAGTTGGAGTATCCCCGATTAAAGGAAAATTGGT
131 TGAAAAAATAATGTTTTTGGAAATAAAATCGGAGTTGGAGTATCCCCGATTAAAGGAAAATTGGT
* *
309950 GTTTTAGAAATAAAATCGGGGTTGGAGTATCCCCGATTATGAATAATT
196 GTTTTAGAAATAAAACCGGGGTTGGAGTATCCCCAATTATGAATAATT
309998 GAGAAACTTA
Statistics
Matches: 227, Mismatches: 13, Indels: 4
0.93 0.05 0.02
Matches are distributed among these distances:
260 183 0.81
261 44 0.19
ACGTcount: A:0.32, C:0.13, G:0.26, T:0.29
Consensus pattern (262 bp):
CGGGGTTGGAGTATCCCCAATTATGAGAAATCAATATTTTGAAAATAAAGCCGGGGTTAGAGTAT
CCCCTCGGAGGTAACGGGGTTAGAGTATCCCCGATGAAATAACGAGGTTGGAGTATCCTCAATTG
TGAAAAAATAATGTTTTTGGAAATAAAATCGGAGTTGGAGTATCCCCGATTAAAGGAAAATTGGT
GTTTTAGAAATAAAACCGGGGTTGGAGTATCCCCAATTATGAATAATTAGTATTTTAGAAATAAA
AT
Found at i:309925 original size:52 final size:51
Alignment explanation
Indices: 309866--309998 Score: 185
Period size: 52 Copynumber: 2.6 Consensus size: 51
309856 AAATAACGAG
* * *
309866 GTTGGAGTATCCTCGATTGTGAAAAATTGGTGTTTTTGGAAATAAAATCGGA
1 GTTGGAGTATCCCCGATTATGAAAAATTGGTG-TTTTAGAAATAAAATCGGA
* * *
309918 GTTGGAGTATCCCCGATTAAAGGAAAATTGGTGTTTTAGAAATAAAATCGGG
1 GTTGGAGTATCCCCGATT-ATGAAAAATTGGTGTTTTAGAAATAAAATCGGA
*
309970 GTTGGAGTATCCCCGATTATGAATAATTG
1 GTTGGAGTATCCCCGATTATGAAAAATTG
309999 AGAAACTTAA
Statistics
Matches: 71, Mismatches: 9, Indels: 3
0.86 0.11 0.04
Matches are distributed among these distances:
51 8 0.11
52 52 0.73
53 11 0.15
ACGTcount: A:0.32, C:0.10, G:0.26, T:0.32
Consensus pattern (51 bp):
GTTGGAGTATCCCCGATTATGAAAAATTGGTGTTTTAGAAATAAAATCGGA
Found at i:312659 original size:28 final size:28
Alignment explanation
Indices: 312397--312694 Score: 210
Period size: 28 Copynumber: 10.6 Consensus size: 28
312387 GGTATCTACA
* *
312397 GTGGGCTTTAAAAGGGTGTCACTGACTT
1 GTGGGCTTTAAAAAGGTGCCACTGACTT
* * *
312425 GTGAGCTTT-AAAAGGTGTCACTAACTT
1 GTGGGCTTTAAAAAGGTGCCACTGACTT
* *
312452 GTGGGCTTTAGAAAAAGTGCCACTAACTT
1 GTGGGCTTTA-AAAAGGTGCCACTGACTT
* * *
312481 GTGGGCTTTAGAAGGGTGCCACTGACTC
1 GTGGGCTTTAAAAAGGTGCCACTGACTT
* *
312509 GTGGGCTTTAAAAGGGTACCACTCG-CTT
1 GTGGGCTTTAAAAAGGTGCCACT-GACTT
* * * *
312537 ATGGCCTTTAAAAAGATG---CTAACTT
1 GTGGGCTTTAAAAAGGTGCCACTGACTT
* * *
312562 GTAGGCTTTAGAATGGTGCCACTGACTT
1 GTGGGCTTTAAAAAGGTGCCACTGACTT
* * * * * **
312590 ATGCGCTTTAGAAGGGTGTCGTTGACTT
1 GTGGGCTTTAAAAAGGTGCCACTGACTT
* * *
312618 GTGGGCTTTGAAAATGTGTCACTGACTT
1 GTGGGCTTTAAAAAGGTGCCACTGACTT
* * *
312646 GTGGGCTTAAAAAAAGGGGATGCCATTGTCTT
1 GTGGGCTT-TAAAAA--GG-TGCCACTGACTT
*
312678 GTGGGCTTTGAAAAGGT
1 GTGGGCTTTAAAAAGGT
312695 ACGATGCCAC
Statistics
Matches: 209, Mismatches: 50, Indels: 22
0.74 0.18 0.08
Matches are distributed among these distances:
25 17 0.08
27 24 0.11
28 113 0.54
29 33 0.16
31 5 0.02
32 17 0.08
ACGTcount: A:0.24, C:0.16, G:0.29, T:0.31
Consensus pattern (28 bp):
GTGGGCTTTAAAAAGGTGCCACTGACTT
Found at i:314068 original size:20 final size:20
Alignment explanation
Indices: 314043--314099 Score: 105
Period size: 20 Copynumber: 2.9 Consensus size: 20
314033 TTTTTACAAT
314043 TTGTATCGATACATTGTTCA
1 TTGTATCGATACATTGTTCA
*
314063 TTGTATCGATACATCGTTCA
1 TTGTATCGATACATTGTTCA
314083 TTGTATCGATACATTGT
1 TTGTATCGATACATTGT
314100 ATCGATACAT
Statistics
Matches: 35, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
20 35 1.00
ACGTcount: A:0.25, C:0.16, G:0.16, T:0.44
Consensus pattern (20 bp):
TTGTATCGATACATTGTTCA
Found at i:314099 original size:13 final size:13
Alignment explanation
Indices: 314081--314110 Score: 60
Period size: 13 Copynumber: 2.3 Consensus size: 13
314071 ATACATCGTT
314081 CATTGTATCGATA
1 CATTGTATCGATA
314094 CATTGTATCGATA
1 CATTGTATCGATA
314107 CATT
1 CATT
314111 CTGGGTTACA
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 17 1.00
ACGTcount: A:0.30, C:0.17, G:0.13, T:0.40
Consensus pattern (13 bp):
CATTGTATCGATA
Found at i:316669 original size:28 final size:28
Alignment explanation
Indices: 316618--316689 Score: 81
Period size: 28 Copynumber: 2.6 Consensus size: 28
316608 TTTTTTCATA
* *
316618 ATCGGGGGTACGCCAATCTCGTTATTTC
1 ATCGGGGATACTCCAATCTCGTTATTTC
* *
316646 ATCGGGGATACTCCACTCTTGTTATTTC
1 ATCGGGGATACTCCAATCTCGTTATTTC
***
316674 CGAGGGGATACTCCAA
1 ATCGGGGATACTCCAA
316690 CCCCGATTTT
Statistics
Matches: 36, Mismatches: 8, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
28 36 1.00
ACGTcount: A:0.21, C:0.25, G:0.24, T:0.31
Consensus pattern (28 bp):
ATCGGGGATACTCCAATCTCGTTATTTC
Found at i:325486 original size:20 final size:20
Alignment explanation
Indices: 325461--325510 Score: 66
Period size: 20 Copynumber: 2.5 Consensus size: 20
325451 ATCGATATCC
**
325461 TATCGATACATTCATTTA-TG
1 TATCGATACA-TCAACTATTG
325481 TATCGATACATCAACTATTG
1 TATCGATACATCAACTATTG
325501 TATCGATACA
1 TATCGATACA
325511 AATTATAGAA
Statistics
Matches: 27, Mismatches: 2, Indels: 2
0.87 0.06 0.06
Matches are distributed among these distances:
19 5 0.19
20 22 0.81
ACGTcount: A:0.34, C:0.18, G:0.10, T:0.38
Consensus pattern (20 bp):
TATCGATACATCAACTATTG
Found at i:328633 original size:29 final size:30
Alignment explanation
Indices: 328600--328663 Score: 76
Period size: 31 Copynumber: 2.1 Consensus size: 30
328590 TTAGTGGCTC
* * *
328600 AAGATTAAACCTTTT-ATTTAAGTTAATTA
1 AAGATGAAACCTTTTAATTTAAATCAATTA
*
328629 AAGATGCAACCTTTTAAATTTAAATCAATTA
1 AAGATGAAACCTTTT-AATTTAAATCAATTA
328660 AAGA
1 AAGA
328664 CATTTGACAA
Statistics
Matches: 29, Mismatches: 4, Indels: 2
0.83 0.11 0.06
Matches are distributed among these distances:
29 13 0.45
31 16 0.55
ACGTcount: A:0.45, C:0.09, G:0.08, T:0.38
Consensus pattern (30 bp):
AAGATGAAACCTTTTAATTTAAATCAATTA
Found at i:329361 original size:13 final size:13
Alignment explanation
Indices: 329343--329368 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
329333 CATTTTTCTG
329343 TGTATCGATACAT
1 TGTATCGATACAT
329356 TGTATCGATACAT
1 TGTATCGATACAT
329369 GGATCTTTGT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.31, C:0.15, G:0.15, T:0.38
Consensus pattern (13 bp):
TGTATCGATACAT
Found at i:329365 original size:33 final size:33
Alignment explanation
Indices: 329323--329389 Score: 98
Period size: 33 Copynumber: 2.0 Consensus size: 33
329313 GCCAAGGAAA
***
329323 TGTATCGATACATTTTTCTGTGTATCGATACAT
1 TGTATCGATACATGGATCTGTGTATCGATACAT
*
329356 TGTATCGATACATGGATCTTTGTATCGATACAT
1 TGTATCGATACATGGATCTGTGTATCGATACAT
329389 T
1 T
329390 TGGGAATTTT
Statistics
Matches: 30, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
33 30 1.00
ACGTcount: A:0.25, C:0.15, G:0.16, T:0.43
Consensus pattern (33 bp):
TGTATCGATACATGGATCTGTGTATCGATACAT
Found at i:331771 original size:51 final size:53
Alignment explanation
Indices: 331714--331836 Score: 162
Period size: 51 Copynumber: 2.4 Consensus size: 53
331704 CAATTCTCCG
* * * *
331714 CAATCGGGGATATTCCATCTCCGATTTTATTTTC-AAAA-CACTAA-TTTTCTA
1 CAATCGGGGATACTCCAACTCCGATTTTATTTCCAAAAAGCACCAATTTTTC-A
* *
331765 TAATCGGGGATACTCTAACTCCGATTTTATTTCCAAAAAGCACCAATTTTTCA
1 CAATCGGGGATACTCCAACTCCGATTTTATTTCCAAAAAGCACCAATTTTTCA
331818 CAATCGGGGATACTCCAAC
1 CAATCGGGGATACTCCAAC
331837 CCCGTTAATC
Statistics
Matches: 61, Mismatches: 8, Indels: 4
0.84 0.11 0.05
Matches are distributed among these distances:
51 29 0.48
52 4 0.07
53 23 0.38
54 5 0.08
ACGTcount: A:0.31, C:0.24, G:0.12, T:0.33
Consensus pattern (53 bp):
CAATCGGGGATACTCCAACTCCGATTTTATTTCCAAAAAGCACCAATTTTTCA
Found at i:331850 original size:27 final size:28
Alignment explanation
Indices: 331820--331893 Score: 96
Period size: 27 Copynumber: 2.7 Consensus size: 28
331810 ATTTTTCACA
*
331820 ATCGGGGATACTCCAACCCCGTTA-ATC
1 ATCGGGGATACTCCAACCCCATTATATC
*
331847 ATCGGGGATACTCCAACCCCATTATTTC
1 ATCGGGGATACTCCAACCCCATTATATC
***
331875 CGAGGGGATACTCCAACCC
1 ATCGGGGATACTCCAACCC
331894 TTGCTTTATT
Statistics
Matches: 41, Mismatches: 5, Indels: 1
0.87 0.11 0.02
Matches are distributed among these distances:
27 23 0.56
28 18 0.44
ACGTcount: A:0.26, C:0.34, G:0.19, T:0.22
Consensus pattern (28 bp):
ATCGGGGATACTCCAACCCCATTATATC
Found at i:331953 original size:51 final size:52
Alignment explanation
Indices: 331878--332099 Score: 191
Period size: 52 Copynumber: 4.3 Consensus size: 52
331868 TTATTTCCGA
** * * * * *
331878 GGGGATACTCCAACCCTTGCTTTATTCTTAAAATATTGATTTCT-CATAATC
1 GGGGATACTCCAACCCCGGTTTTATTCTTAAAACACTAATTTCTCCACAATC
* *
331929 GGGGATACTCAAACCCCGGTTTTATTGC-TAAAACACTAATTTTTCCACAATC
1 GGGGATACTCCAACCCCGGTTTTATT-CTTAAAACACTAATTTCTCCACAATC
* * **
331981 GGGGATACTCCAACCCCGGTTTTATTTTTAAAACACAAATTT-TCCTTTAATC
1 GGGGATACTCCAACCCCGGTTTTATTCTTAAAACACTAATTTCTCC-ACAATC
* * * * ** * *
332033 GAGGATACTCCAGCTCCGATTTTACTTCCAAAAACACCAATTT-TTCACAATC
1 GGGGATACTCCAACCCCGGTTTTA-TTCTTAAAACACTAATTTCTCCACAATC
*
332085 GAGGATACTCCAACC
1 GGGGATACTCCAACC
332100 TCGTTATTTC
Statistics
Matches: 139, Mismatches: 27, Indels: 9
0.79 0.15 0.05
Matches are distributed among these distances:
51 37 0.27
52 86 0.62
53 16 0.12
ACGTcount: A:0.30, C:0.25, G:0.12, T:0.32
Consensus pattern (52 bp):
GGGGATACTCCAACCCCGGTTTTATTCTTAAAACACTAATTTCTCCACAATC
Found at i:332110 original size:31 final size:28
Alignment explanation
Indices: 332082--332158 Score: 86
Period size: 28 Copynumber: 2.8 Consensus size: 28
332072 ATTTTTCACA
*
332082 ATCGAGGATACTCCAACCTCGTTATTTC
1 ATCGAGGATACTCCAACCCCGTTATTTC
* **
332110 ATCGGGGATACTCCAACCCCGTTACCTC
1 ATCGAGGATACTCCAACCCCGTTATTTC
332138 --CGAGGGGATACTCCAACCCCG
1 ATCGA--GGATACTCCAACCCCG
332159 GCTTTATTCC
Statistics
Matches: 42, Mismatches: 5, Indels: 4
0.82 0.10 0.08
Matches are distributed among these distances:
26 2 0.05
28 40 0.95
ACGTcount: A:0.23, C:0.35, G:0.19, T:0.22
Consensus pattern (28 bp):
ATCGAGGATACTCCAACCCCGTTATTTC
Found at i:332180 original size:263 final size:262
Alignment explanation
Indices: 331714--332206 Score: 754
Period size: 263 Copynumber: 1.9 Consensus size: 262
331704 CAATTCTCCG
* * * * *
331714 CAATCGGGGATATTCCATCTCCGATTTTATTTTCAAAACACTAATTTTCTATAATCGGGGATACT
1 CAATCGGGGATACTCCAACCCCGATTTTATTTTCAAAACACAAATTTTCTATAATCGAGGATACT
* * *
331779 CTAACTCCGATTTTATTTCCAAAAAGCACCAATTTTTCACAATCGGGGATACTCCAACCCCGTTA
66 CCAACTCCGATTTTACTTCCAAAAAGCACCAATTTTTCACAATCGAGGATACTCCAACCCCGTTA
** ** **
331844 ATCATCGGGGATACTCCAACCCCATTATTTCCGAGGGGATACTCCAACCCTTGCTTTATTCTTAA
131 ATCATCGGGGATACTCCAACCCCATTACCTCCGAGGGGATACTCCAACCCCGGCTTTATTCCCAA
331909 AATATTGATTTCTCATAATCGGGGATACTCAAACCCCGGTTTTATTGCTAAAACACTAATTTTTC
196 AATATTGATTTCTCATAATCGGGGATACTCAAACCCCGGTTTTATTGCTAAAACACTAATTTTTC
331974 CA
261 CA
* * *
331976 CAATCGGGGATACTCCAACCCCGGTTTTATTTTTAAAACACAAATTTTCCTTTAATCGAGGATAC
1 CAATCGGGGATACTCCAACCCCGATTTTATTTTCAAAACACAAATTTT-CTATAATCGAGGATAC
* *
332041 TCCAGCTCCGATTTTACTTCCAAAAA-CACCAATTTTTCACAATCGAGGATACTCCAACCTCGTT
65 TCCAACTCCGATTTTACTTCCAAAAAGCACCAATTTTTCACAATCGAGGATACTCCAACCCCGTT
* *
332105 ATTTCATCGGGGATACTCCAACCCCGTTACCTCCGAGGGGATACTCCAACCCCGGCTTTATTCCC
130 A-ATCATCGGGGATACTCCAACCCCATTACCTCCGAGGGGATACTCCAACCCCGGCTTTATTCCC
* *
332170 AAAATATTGATTTCTCATAATTGGGGATACTCCAACC
194 AAAATATTGATTTCTCATAATCGGGGATACTCAAACC
332207 TCGTTATTTC
Statistics
Matches: 206, Mismatches: 23, Indels: 3
0.89 0.10 0.01
Matches are distributed among these distances:
262 79 0.38
263 127 0.62
ACGTcount: A:0.29, C:0.27, G:0.13, T:0.31
Consensus pattern (262 bp):
CAATCGGGGATACTCCAACCCCGATTTTATTTTCAAAACACAAATTTTCTATAATCGAGGATACT
CCAACTCCGATTTTACTTCCAAAAAGCACCAATTTTTCACAATCGAGGATACTCCAACCCCGTTA
ATCATCGGGGATACTCCAACCCCATTACCTCCGAGGGGATACTCCAACCCCGGCTTTATTCCCAA
AATATTGATTTCTCATAATCGGGGATACTCAAACCCCGGTTTTATTGCTAAAACACTAATTTTTC
CA
Found at i:346751 original size:13 final size:13
Alignment explanation
Indices: 346726--346759 Score: 59
Period size: 13 Copynumber: 2.5 Consensus size: 13
346716 AAAAAAGCAA
346726 AAAAAAACAAAAC
1 AAAAAAACAAAAC
346739 AAAAAAACAAAAC
1 AAAAAAACAAAAC
346752 AAAGAAAA
1 AAA-AAAA
346760 AGAGAGAAAA
Statistics
Matches: 20, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
13 16 0.80
14 4 0.20
ACGTcount: A:0.85, C:0.12, G:0.03, T:0.00
Consensus pattern (13 bp):
AAAAAAACAAAAC
Found at i:347851 original size:59 final size:59
Alignment explanation
Indices: 347745--349172 Score: 2345
Period size: 59 Copynumber: 24.2 Consensus size: 59
347735 TCCACTTTTT
* * * *
347745 AGTCCTCAAAGAGCAGGATGCCTGTTCCTCTTAAAGCCCACACAAGTTGGTGGCACCTTC
1 AGTCCTCAAAGAGCGGGACGCCT-TTTCTTTTAAAGCCCACACAAGTTGGTGGCACCTTC
* *
347805 AGTCCTCAAAGAGCAGGACACCTTTTCTTTTAAAGCCCACACAAGTTGGTGGCACCTTC
1 AGTCCTCAAAGAGCGGGACGCCTTTTCTTTTAAAGCCCACACAAGTTGGTGGCACCTTC
347864 AGTCCTCAAAGAGCGGGACGCCTTTTCTTTTAAAGCCCACACAAGTTGGTGGCACCTTC
1 AGTCCTCAAAGAGCGGGACGCCTTTTCTTTTAAAGCCCACACAAGTTGGTGGCACCTTC
* *
347923 AGTCCTCAAAGAGCGGGACGCCTTTTCTTTTAAAGCCCACCCAAGTTGGTGGCACATTTC
1 AGTCCTCAAAGAGCGGGACGCCTTTTCTTTTAAAGCCCACACAAGTTGGTGGCAC-CTTC
* *
347983 AGTCCCCAAAGAGCGGGACGCCTTTTCTTTTAAAGCCTACACAAGTTGGTGGCACCTTTC
1 AGTCCTCAAAGAGCGGGACGCCTTTTCTTTTAAAGCCCACACAAGTTGGTGGCACC-TTC
* *
348043 AGTCCCCAAAGAGCGGGACGCCTTTTCTTTTAAAGCCCACCCAAGTTGGTGGCACCTTTC
1 AGTCCTCAAAGAGCGGGACGCCTTTTCTTTTAAAGCCCACACAAGTTGGTGGCACC-TTC
* *
348103 AGTCCCCAAAGAGCGGGACGCCTTTTCTTTTAAAGCCTACACAAGTTGGTGGCACCTGTC
1 AGTCCTCAAAGAGCGGGACGCCTTTTCTTTTAAAGCCCACACAAGTTGGTGGCACCT-TC
* *
348163 AGTCCCCAAAGAGCGGGACGCCTTTTCTTTTAAAGCCTACACAAGTTGGTGGCACCTTC
1 AGTCCTCAAAGAGCGGGACGCCTTTTCTTTTAAAGCCCACACAAGTTGGTGGCACCTTC
*
348222 AGTCCTCAAAGAGCGGGATGCCTTTTCTTTTAAAGCCCACACAAGTTGGTGGCACCTTC
1 AGTCCTCAAAGAGCGGGACGCCTTTTCTTTTAAAGCCCACACAAGTTGGTGGCACCTTC
* *
348281 AGTCCTCAAAGAGCGGGACGCCTTTTCTTTTAAAGCCTACACAAGTTGGTGGCACTTTC
1 AGTCCTCAAAGAGCGGGACGCCTTTTCTTTTAAAGCCCACACAAGTTGGTGGCACCTTC
348340 AGTCCTCAAAGAGCGGGACGCCTTTTCTTTTAAAGCCCACACAAGTTGGTGGCACCTTC
1 AGTCCTCAAAGAGCGGGACGCCTTTTCTTTTAAAGCCCACACAAGTTGGTGGCACCTTC
* * * *
348399 AGTCCTCAAAGAGTGGGACACCTTTTCTATTAAAGCCCACACAAGTTGGTGGAACCTTC
1 AGTCCTCAAAGAGCGGGACGCCTTTTCTTTTAAAGCCCACACAAGTTGGTGGCACCTTC
* *
348458 AGTCCTCAAAGAGCAGGACACCTTTTCTTTTAAAGCCCACACAAGTTGGTGGCACCTTC
1 AGTCCTCAAAGAGCGGGACGCCTTTTCTTTTAAAGCCCACACAAGTTGGTGGCACCTTC
* *
348517 AGTCCTCAAAGAACGGGACACCTTTTCTTTTAAAGCCCACACAAGTTGGTGGCACCTTC
1 AGTCCTCAAAGAGCGGGACGCCTTTTCTTTTAAAGCCCACACAAGTTGGTGGCACCTTC
* *
348576 AGTCCTTAAAGAGCAGGACGCCTTTTCTTTTAAAGCCCACACAAGTTGGTGGCACCTTC
1 AGTCCTCAAAGAGCGGGACGCCTTTTCTTTTAAAGCCCACACAAGTTGGTGGCACCTTC
348635 AGTCCTCAAAGAGCGGGACGCCTTTTCTTTTAAAGCCCACACAAGTTGGTGGCACCTTC
1 AGTCCTCAAAGAGCGGGACGCCTTTTCTTTTAAAGCCCACACAAGTTGGTGGCACCTTC
*
348694 AGTCCTCAAAGAGCGGGACACCTTTTCTTTTAAAGCCCACACAAGTTGGTGGCACCTTC
1 AGTCCTCAAAGAGCGGGACGCCTTTTCTTTTAAAGCCCACACAAGTTGGTGGCACCTTC
* *
348753 AGTCCTTAAAGAGCAGGACGCCTTTTCTTTTAAAGCCCACACAAGTTGGTGGCACCTTC
1 AGTCCTCAAAGAGCGGGACGCCTTTTCTTTTAAAGCCCACACAAGTTGGTGGCACCTTC
*
348812 AGTCCTCAAAGAGCAGGACGCCTTTTCTTTTAAAGCCCACACAAGTTGGTGGCACCTTC
1 AGTCCTCAAAGAGCGGGACGCCTTTTCTTTTAAAGCCCACACAAGTTGGTGGCACCTTC
348871 AGTCCTCAAAGAGCGGGACGCCTTTTCTTTTAAAGCCCACACAAGTTGGTGGCACCTTC
1 AGTCCTCAAAGAGCGGGACGCCTTTTCTTTTAAAGCCCACACAAGTTGGTGGCACCTTC
348930 AGTCCTCAAAGAGCGGGACGCCTTTTCTTTTAAAGCCCACACAAGTTGGTGGCACCTTC
1 AGTCCTCAAAGAGCGGGACGCCTTTTCTTTTAAAGCCCACACAAGTTGGTGGCACCTTC
* *
348989 AGTCCTCAAAGAGCAGGACGCCTTTTCTTTTAAAGCCCACACAAGTTGGTGGCACCTTTT
1 AGTCCTCAAAGAGCGGGACGCCTTTTCTTTTAAAGCCCACACAAGTTGGTGGCACC-TTC
*
349049 AGTCCTCAAAGAGCAGGACGCC-TTTC----AAAGCCCACACAAGTTGGTGGCACCTTTC
1 AGTCCTCAAAGAGCGGGACGCCTTTTCTTTTAAAGCCCACACAAGTTGGTGGCACC-TTC
* * * * *
349104 AGTCCTCAAAGAACAGGACGCC-TTTC----AAAGCCCACACGAGTTGGTGGCACTTTTT
1 AGTCCTCAAAGAGCGGGACGCCTTTTCTTTTAAAGCCCACACAAGTTGGTGGCAC-CTTC
349159 AGTCCTCAAAGAGC
1 AGTCCTCAAAGAGC
349173 AGGATACACT
Statistics
Matches: 1309, Mismatches: 54, Indels: 15
0.95 0.04 0.01
Matches are distributed among these distances:
55 91 0.07
59 944 0.72
60 274 0.21
ACGTcount: A:0.25, C:0.28, G:0.21, T:0.25
Consensus pattern (59 bp):
AGTCCTCAAAGAGCGGGACGCCTTTTCTTTTAAAGCCCACACAAGTTGGTGGCACCTTC
Found at i:351646 original size:29 final size:30
Alignment explanation
Indices: 351613--351676 Score: 76
Period size: 31 Copynumber: 2.1 Consensus size: 30
351603 TTAGTGGCTC
* * *
351613 AAGATTAAACCTTTT-ATTTAAGTTAATTA
1 AAGATGAAACCTTTTAATTTAAATCAATTA
*
351642 AAGATGCAACCTTTTAAATTTAAATCAATTA
1 AAGATGAAACCTTTT-AATTTAAATCAATTA
351673 AAGA
1 AAGA
351677 CATTTGACAA
Statistics
Matches: 29, Mismatches: 4, Indels: 2
0.83 0.11 0.06
Matches are distributed among these distances:
29 13 0.45
31 16 0.55
ACGTcount: A:0.45, C:0.09, G:0.08, T:0.38
Consensus pattern (30 bp):
AAGATGAAACCTTTTAATTTAAATCAATTA
Found at i:352377 original size:33 final size:33
Alignment explanation
Indices: 352334--352400 Score: 89
Period size: 33 Copynumber: 2.0 Consensus size: 33
352324 GCCAAGGAAA
***
352334 TGTATCGATACATTTTTCTGTGTATCGATACAT
1 TGTATCGATACATGGATCTGTGTATCGATACAT
* *
352367 TGTATTGATACATGGATCTTTGTATCGATACAT
1 TGTATCGATACATGGATCTGTGTATCGATACAT
352400 T
1 T
352401 TGGGAATTTT
Statistics
Matches: 29, Mismatches: 5, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
33 29 1.00
ACGTcount: A:0.25, C:0.13, G:0.16, T:0.45
Consensus pattern (33 bp):
TGTATCGATACATGGATCTGTGTATCGATACAT
Found at i:352926 original size:10 final size:10
Alignment explanation
Indices: 352911--352944 Score: 50
Period size: 10 Copynumber: 3.3 Consensus size: 10
352901 AATCCTTTAG
352911 CAAAAAAAAC
1 CAAAAAAAAC
352921 CAAAAAAACAC
1 CAAAAAAA-AC
*
352932 AAAAAAAAAC
1 CAAAAAAAAC
352942 CAA
1 CAA
352945 GCTTCATCCT
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
10 12 0.57
11 9 0.43
ACGTcount: A:0.79, C:0.21, G:0.00, T:0.00
Consensus pattern (10 bp):
CAAAAAAAAC
Found at i:352926 original size:11 final size:11
Alignment explanation
Indices: 352912--352944 Score: 50
Period size: 11 Copynumber: 3.1 Consensus size: 11
352902 ATCCTTTAGC
352912 AAAAAAAACCA
1 AAAAAAAACCA
*
352923 AAAAAACA-CA
1 AAAAAAAACCA
352933 AAAAAAAACCA
1 AAAAAAAACCA
352944 A
1 A
352945 GCTTCATCCT
Statistics
Matches: 19, Mismatches: 2, Indels: 2
0.83 0.09 0.09
Matches are distributed among these distances:
10 9 0.47
11 10 0.53
ACGTcount: A:0.82, C:0.18, G:0.00, T:0.00
Consensus pattern (11 bp):
AAAAAAAACCA
Found at i:354669 original size:51 final size:53
Alignment explanation
Indices: 354613--354734 Score: 169
Period size: 51 Copynumber: 2.3 Consensus size: 53
354603 AATTCTCCAC
* * * * *
354613 AATCGGGGATATTCCATCTCCGATTTTATTTTC-AAAA-CACTAA-TTTTCTAT
1 AATCGGGGATACTCCAACTCCGATTTTATTTCCAAAAAGCACCAATTTTTC-AA
354664 AATCGGGGATACTCCAACTCCGATTTTATTTCCAAAAAGCACCAATTTTTCAA
1 AATCGGGGATACTCCAACTCCGATTTTATTTCCAAAAAGCACCAATTTTTCAA
354717 AATCGGGGATACTCCAAC
1 AATCGGGGATACTCCAAC
354735 CCCGTTAATC
Statistics
Matches: 63, Mismatches: 5, Indels: 4
0.88 0.07 0.06
Matches are distributed among these distances:
51 30 0.48
52 4 0.06
53 24 0.38
54 5 0.08
ACGTcount: A:0.32, C:0.23, G:0.12, T:0.33
Consensus pattern (53 bp):
AATCGGGGATACTCCAACTCCGATTTTATTTCCAAAAAGCACCAATTTTTCAA
Found at i:354729 original size:53 final size:51
Alignment explanation
Indices: 354613--354997 Score: 183
Period size: 52 Copynumber: 7.4 Consensus size: 51
354603 AATTCTCCAC
* * * * *
354613 AATCGGGGATATTCCATCTCCGATTTTATTTTCAAAACACTAATTTTCTAT
1 AATCGGGGATACTCCAACTCCGATTTTATTTCCAAAACACCAATTTTCTAA
354664 AATCGGGGATACTCCAACTCCGATTTTATTTCCAAAAAGCACCAATTTT-TCAA
1 AATCGGGGATACTCCAACTCCGATTTTATTTCC-AAAA-CACCAATTTTCT-AA
* * * ** * * ** *
354717 AATCGGGGATACTCCAACCCCG--TTAATCATCGGGGATACTCCAA-CCTCGTTA
1 AATCGGGGATACTCCAACTCCGATTTTAT-TTC--CAAAACACCAATTTTC-TAA
** * * * * *** *
354769 TTTCCGAGGGGATACTCCAACCCCTG-CTTTA-TTCTTAAAATATTGA-TTTCTCAT
1 AAT-C--GGGGATACTCCAACTCC-GATTTTATTTC-CAAAACACCAATTTTCT-AA
* * * * * * *
354823 AATCGGGGATACTCCAAC-CTCGGTTTTACTGCTAAAACACTAATTTTTCCAC
1 AATCGGGGATACTCCAACTC-CGATTTTATTTCCAAAACACCAA-TTTTCTAA
* ** **
354875 AATCGGGGATACTCCAACCCCGATTTTATTTTTAAAACACCAATTTTCCTTT
1 AATCGGGGATACTCCAACTCCGATTTTATTTCCAAAACACCAATTTT-CTAA
* * *
354927 AATCGGGGATACTCCAGCTCTGATTTTATTTCCAAAAACACCAATTTTTTAA
1 AATCGGGGATACTCCAACTCCGATTTTATTTCC-AAAACACCAATTTTCTAA
*
354979 CAATCGAGGATACTCCAAC
1 -AATCGGGGATACTCCAAC
354998 CTCATTATTT
Statistics
Matches: 252, Mismatches: 59, Indels: 44
0.71 0.17 0.12
Matches are distributed among these distances:
50 2 0.01
51 66 0.26
52 83 0.33
53 72 0.29
54 6 0.02
55 19 0.08
56 1 0.00
57 3 0.01
ACGTcount: A:0.30, C:0.25, G:0.13, T:0.33
Consensus pattern (51 bp):
AATCGGGGATACTCCAACTCCGATTTTATTTCCAAAACACCAATTTTCTAA
Found at i:354748 original size:27 final size:28
Alignment explanation
Indices: 354718--354792 Score: 98
Period size: 27 Copynumber: 2.7 Consensus size: 28
354708 ATTTTTCAAA
354718 ATCGGGGATACTCCAACCCCGTTA-ATC
1 ATCGGGGATACTCCAACCCCGTTATATC
* *
354745 ATCGGGGATACTCCAACCTCGTTATTTC
1 ATCGGGGATACTCCAACCCCGTTATATC
***
354773 CGAGGGGATACTCCAACCCC
1 ATCGGGGATACTCCAACCCC
354793 TGCTTTATTC
Statistics
Matches: 41, Mismatches: 6, Indels: 1
0.85 0.12 0.02
Matches are distributed among these distances:
27 23 0.56
28 18 0.44
ACGTcount: A:0.24, C:0.33, G:0.20, T:0.23
Consensus pattern (28 bp):
ATCGGGGATACTCCAACCCCGTTATATC
Found at i:354892 original size:52 final size:52
Alignment explanation
Indices: 354823--355000 Score: 189
Period size: 52 Copynumber: 3.4 Consensus size: 52
354813 GATTTCTCAT
* * * *
354823 AATCGGGGATACTCCAACCTCGGTTTTACTGCTAAAACACTAATTTTTCCAC
1 AATCGGGGATACTCCAACCTCGATTTTATTCCTAAAACACCAATTTTTCCAC
* ** **
354875 AATCGGGGATACTCCAACCCCGATTTTATTTTTAAAACACCAA-TTTTCCTTT
1 AATCGGGGATACTCCAACCTCGATTTTATTCCTAAAACACCAATTTTTCC-AC
* * **
354927 AATCGGGGATACTCC-AGCTCTGATTTTATTTCCAAAAACACCAATTTTTTAAC
1 AATCGGGGATACTCCAACCTC-GATTTTA-TTCCTAAAACACCAATTTTTCCAC
*
354980 AATCGAGGATACTCCAACCTC
1 AATCGGGGATACTCCAACCTC
355001 ATTATTTCAT
Statistics
Matches: 102, Mismatches: 19, Indels: 8
0.79 0.15 0.06
Matches are distributed among these distances:
51 9 0.09
52 59 0.58
53 26 0.25
54 8 0.08
ACGTcount: A:0.30, C:0.26, G:0.12, T:0.32
Consensus pattern (52 bp):
AATCGGGGATACTCCAACCTCGATTTTATTCCTAAAACACCAATTTTTCCAC
Found at i:355077 original size:264 final size:262
Alignment explanation
Indices: 354608--355103 Score: 769
Period size: 264 Copynumber: 1.9 Consensus size: 262
354598 TTCTCAATTC
* * * *
354608 TCCACAATCGGGGATATTCCATCTCCGATTTTATTTTCAAAACACTAATTTTCTATAATCGGGGA
1 TCCACAATCGGGGATACTCCAACCCCGATTTTATTTTCAAAACACCAATTTTCTATAATCGGGGA
*
354673 TACTCCAACTCCGATTTTATTTCCAAAAAGCACCAATTTTTCAAAATCGGGGATACTCCAACCCC
66 TACTCCAACTCCGATTTTATTTCCAAAAAGCACCAATTTTTCAAAATCGAGGATACTCCAACCCC
* * ** * *
354738 GTTAATCATCGGGGATACTCCAACCTCGTTATTTCCGAGGGGATACTCCAACCCCTGCTTTATTC
131 ATTAATCATCGGGGATACTCCAACCCCGTTACCTCCGAAGGGATACTCCAACCCCGGCTTTATTC
**
354803 TTAAAATATTGATTTCTCATAATCGGGGATACTCCAACCTCGGTTTTACTGCTAAAACACTAATT
196 CCAAAATATTGATTTCTCATAATCGGGGATACTCCAACCTCGGTTTTACTGCTAAAACACTAATT
354868 TT
261 TT
* *
354870 TCCACAATCGGGGATACTCCAACCCCGATTTTATTTTTAAAACACCAATTTTCCTTTAATCGGGG
1 TCCACAATCGGGGATACTCCAACCCCGATTTTATTTTCAAAACACCAATTTT-CTATAATCGGGG
* * *
354935 ATACTCCAGCTCTGATTTTATTTCCAAAAA-CACCAATTTTTTAACAATCGAGGATACTCCAACC
65 ATACTCCAACTCCGATTTTATTTCCAAAAAGCACCAATTTTTCAA-AATCGAGGATACTCCAACC
* *
354999 TCATTATTTCATCGGGGATACTCCAACCCCGTTACCTCCGAAGGGATACTCCAACCCCGGCTTTA
129 CCATTA-ATCATCGGGGATACTCCAACCCCGTTACCTCCGAAGGGATACTCCAACCCCGGCTTTA
*
355064 TTCCCAAAATATTGATTTCTCATAATTGGGGATACTCCAA
193 TTCCCAAAATATTGATTTCTCATAATCGGGGATACTCCAA
355104 TCCCGTTATT
Statistics
Matches: 210, Mismatches: 21, Indels: 4
0.89 0.09 0.02
Matches are distributed among these distances:
262 60 0.29
263 61 0.29
264 89 0.42
ACGTcount: A:0.29, C:0.26, G:0.13, T:0.32
Consensus pattern (262 bp):
TCCACAATCGGGGATACTCCAACCCCGATTTTATTTTCAAAACACCAATTTTCTATAATCGGGGA
TACTCCAACTCCGATTTTATTTCCAAAAAGCACCAATTTTTCAAAATCGAGGATACTCCAACCCC
ATTAATCATCGGGGATACTCCAACCCCGTTACCTCCGAAGGGATACTCCAACCCCGGCTTTATTC
CCAAAATATTGATTTCTCATAATCGGGGATACTCCAACCTCGGTTTTACTGCTAAAACACTAATT
TT
Found at i:358697 original size:59 final size:59
Alignment explanation
Indices: 358627--358739 Score: 174
Period size: 59 Copynumber: 1.9 Consensus size: 59
358617 CAAGAAATTT
*
358627 ATCATGAAAAATGA-TCTAAATGACTCAAAAAATACATGAAATTACATAAAAATCGTTAG
1 ATCATGAAAAATAACT-TAAATGACTCAAAAAATACATGAAATTACATAAAAATCGTTAG
* * *
358686 ATCATGAAAAATAACTTAAATGACTCTAAAAATATATGAAATTGCATAAAAATC
1 ATCATGAAAAATAACTTAAATGACTCAAAAAATACATGAAATTACATAAAAATC
358740 CCTAAGTCAT
Statistics
Matches: 49, Mismatches: 4, Indels: 2
0.89 0.07 0.04
Matches are distributed among these distances:
59 48 0.98
60 1 0.02
ACGTcount: A:0.53, C:0.12, G:0.09, T:0.27
Consensus pattern (59 bp):
ATCATGAAAAATAACTTAAATGACTCAAAAAATACATGAAATTACATAAAAATCGTTAG
Found at i:358768 original size:59 final size:58
Alignment explanation
Indices: 358627--358768 Score: 171
Period size: 59 Copynumber: 2.4 Consensus size: 58
358617 CAAGAAATTT
* *
358627 ATCATGAAAAATGATCTAAATGACTCAAAAAATACATGAAATTACATAAAAATCGTTAG
1 ATCATGAAAAATGA-CTAAATGACTCAAAAAATACATGAAATTACATAAAAATCCTAAG
* * * *
358686 ATCATGAAAAATAACTTAAATGACTCTAAAAATATATGAAATTGCATAAAAATCCCTAAG
1 ATCATGAAAAATGAC-TAAATGACTCAAAAAATACATGAAATTACATAAAAAT-CCTAAG
358746 -TCAT-AGAAAATGACTAAGATGAC
1 ATCATGA-AAAATGACTAA-ATGAC
358769 AAAAAACTCT
Statistics
Matches: 72, Mismatches: 7, Indels: 8
0.83 0.08 0.09
Matches are distributed among these distances:
58 5 0.07
59 63 0.88
60 4 0.06
ACGTcount: A:0.51, C:0.13, G:0.11, T:0.25
Consensus pattern (58 bp):
ATCATGAAAAATGACTAAATGACTCAAAAAATACATGAAATTACATAAAAATCCTAAG
Found at i:358774 original size:19 final size:18
Alignment explanation
Indices: 358759--358798 Score: 80
Period size: 18 Copynumber: 2.2 Consensus size: 18
358749 TAGAAAATGA
358759 CTAAGATGACAAAAAACT
1 CTAAGATGACAAAAAACT
358777 CTAAGATGACAAAAAACT
1 CTAAGATGACAAAAAACT
358795 CTAA
1 CTAA
358799 ATCATGAAAA
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 22 1.00
ACGTcount: A:0.55, C:0.17, G:0.10, T:0.17
Consensus pattern (18 bp):
CTAAGATGACAAAAAACT
Found at i:367903 original size:18 final size:18
Alignment explanation
Indices: 367880--367925 Score: 65
Period size: 19 Copynumber: 2.5 Consensus size: 18
367870 TATTAGATGT
367880 AAAAAATAAATTTAAATA
1 AAAAAATAAATTTAAATA
**
367898 AAAAAATTAAATTTATTTA
1 AAAAAA-TAAATTTAAATA
367917 AAAAAATAA
1 AAAAAATAA
367926 TCAAGCTTTG
Statistics
Matches: 25, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
18 9 0.36
19 16 0.64
ACGTcount: A:0.70, C:0.00, G:0.00, T:0.30
Consensus pattern (18 bp):
AAAAAATAAATTTAAATA
Found at i:368960 original size:22 final size:22
Alignment explanation
Indices: 368932--368973 Score: 68
Period size: 22 Copynumber: 1.9 Consensus size: 22
368922 TCAAAAAAGA
368932 ATTTAAACAAAA-AATTAAGCTC
1 ATTTAAA-AAAAGAATTAAGCTC
368954 ATTTAAAAAAAGAATTAAGC
1 ATTTAAAAAAAGAATTAAGC
368974 CTTGGCTTTC
Statistics
Matches: 19, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
21 4 0.21
22 15 0.79
ACGTcount: A:0.57, C:0.10, G:0.07, T:0.26
Consensus pattern (22 bp):
ATTTAAAAAAAGAATTAAGCTC
Found at i:370042 original size:15 final size:15
Alignment explanation
Indices: 370022--370065 Score: 56
Period size: 15 Copynumber: 3.1 Consensus size: 15
370012 TTTTTTATTT
370022 TTTATATATTATAAA
1 TTTATATATTATAAA
*
370037 TTTATATCTTATAAA
1 TTTATATATTATAAA
*
370052 --TATATAATATAAA
1 TTTATATATTATAAA
370065 T
1 T
370066 ATTAAAAAAT
Statistics
Matches: 25, Mismatches: 3, Indels: 3
0.81 0.10 0.10
Matches are distributed among these distances:
13 11 0.44
15 14 0.56
ACGTcount: A:0.48, C:0.02, G:0.00, T:0.50
Consensus pattern (15 bp):
TTTATATATTATAAA
Found at i:370055 original size:13 final size:13
Alignment explanation
Indices: 370024--370067 Score: 52
Period size: 13 Copynumber: 3.2 Consensus size: 13
370014 TTTTATTTTT
370024 TATATATTATAAA
1 TATATATTATAAA
*
370037 TTTATATCTTATAAA
1 --TATATATTATAAA
*
370052 TATATAATATAAA
1 TATATATTATAAA
370065 TAT
1 TAT
370068 TAAAAAATAT
Statistics
Matches: 26, Mismatches: 3, Indels: 2
0.84 0.10 0.06
Matches are distributed among these distances:
13 14 0.54
15 12 0.46
ACGTcount: A:0.50, C:0.02, G:0.00, T:0.48
Consensus pattern (13 bp):
TATATATTATAAA
Found at i:370947 original size:21 final size:22
Alignment explanation
Indices: 370922--370964 Score: 63
Period size: 21 Copynumber: 2.0 Consensus size: 22
370912 ATTATTTTAC
370922 ATGTTATA-ATTATCTTT-TAAA
1 ATGTTATATA-TATCTTTATAAA
370943 ATGTTATATATATCTTTATAAA
1 ATGTTATATATATCTTTATAAA
370965 TTTTGATTAG
Statistics
Matches: 20, Mismatches: 0, Indels: 3
0.87 0.00 0.13
Matches are distributed among these distances:
21 15 0.75
22 5 0.25
ACGTcount: A:0.40, C:0.05, G:0.05, T:0.51
Consensus pattern (22 bp):
ATGTTATATATATCTTTATAAA
Found at i:371011 original size:32 final size:33
Alignment explanation
Indices: 370959--371026 Score: 86
Period size: 32 Copynumber: 2.1 Consensus size: 33
370949 TATATATCTT
*
370959 TATAAATTTTGATTAGTTAATA-ATTCAAATTA
1 TATAAATTTTGATTAATTAATATATTCAAATTA
* *
370991 TATAAATTTTGA-TACATTAATATATTTATATTA
1 TATAAATTTTGATTA-ATTAATATATTCAAATTA
371024 TAT
1 TAT
371027 TCTTTTTATT
Statistics
Matches: 31, Mismatches: 3, Indels: 3
0.84 0.08 0.08
Matches are distributed among these distances:
31 2 0.06
32 18 0.58
33 11 0.35
ACGTcount: A:0.43, C:0.03, G:0.04, T:0.50
Consensus pattern (33 bp):
TATAAATTTTGATTAATTAATATATTCAAATTA
Found at i:371092 original size:18 final size:18
Alignment explanation
Indices: 371031--371094 Score: 65
Period size: 18 Copynumber: 3.4 Consensus size: 18
371021 TTATATTCTT
*
371031 TTTATTTTTTCATATCGTA
1 TTTATTTTTT-ATATCATA
*
371050 TTATATTTTATTATATTATA
1 TT-TATTTT-TTATATCATA
* *
371070 ATTATTTTTTATATCATG
1 TTTATTTTTTATATCATA
371088 TTTATTT
1 TTTATTT
371095 ATATAATTTT
Statistics
Matches: 37, Mismatches: 6, Indels: 5
0.77 0.12 0.10
Matches are distributed among these distances:
18 14 0.38
19 8 0.22
20 13 0.35
21 2 0.05
ACGTcount: A:0.27, C:0.05, G:0.03, T:0.66
Consensus pattern (18 bp):
TTTATTTTTTATATCATA
Found at i:373828 original size:21 final size:20
Alignment explanation
Indices: 373804--373849 Score: 56
Period size: 21 Copynumber: 2.2 Consensus size: 20
373794 TGTATAAAAT
* *
373804 AAATATGATAAAAAATAATTA
1 AAATATAATAAAAAAT-ATAA
*
373825 AAATATAATATAAAATATAA
1 AAATATAATAAAAAATATAA
373845 AAATA
1 AAATA
373850 ATATTAATTT
Statistics
Matches: 22, Mismatches: 3, Indels: 1
0.85 0.12 0.04
Matches are distributed among these distances:
20 8 0.36
21 14 0.64
ACGTcount: A:0.70, C:0.00, G:0.02, T:0.28
Consensus pattern (20 bp):
AAATATAATAAAAAATATAA
Found at i:373892 original size:25 final size:23
Alignment explanation
Indices: 373831--373960 Score: 87
Period size: 24 Copynumber: 5.5 Consensus size: 23
373821 ATTAAAATAT
373831 AATA-TAAAATATAAAAATAATATT-
1 AATATTAAAATAT--AAAT-ATATTA
373855 AAT-TTAAACATATAAATATATTA
1 AATATTAAA-ATATAAATATATTA
*
373878 AATTTTAAATAATATAAAT-TATTA
1 AATATT-AA-AATATAAATATATTA
*
373902 ATATATTAAAATATATAATATTTTA
1 A-ATATTAAAATATA-AATATATTA
373927 AATA--AAATTATATAAA-ATATATA
1 AATATTAAA--ATATAAATATAT-TA
373950 AATA-TAAAATA
1 AATATTAAAATA
373961 AAAACATTCA
Statistics
Matches: 90, Mismatches: 3, Indels: 28
0.74 0.02 0.23
Matches are distributed among these distances:
22 14 0.16
23 21 0.23
24 31 0.34
25 23 0.26
26 1 0.01
ACGTcount: A:0.60, C:0.01, G:0.00, T:0.39
Consensus pattern (23 bp):
AATATTAAAATATAAATATATTA
Found at i:373922 original size:15 final size:16
Alignment explanation
Indices: 373831--373960 Score: 80
Period size: 16 Copynumber: 8.2 Consensus size: 16
373821 ATTAAAATAT
*
373831 AATATAAAATATA-AA
1 AATATATAATATATAA
373846 AATAATATTAAT-T-TAA
1 AAT-ATA-TAATATATAA
*
373862 ACATATA-AATATATTA
1 A-ATATATAATATATAA
*
373878 AAT-TTTAAATAATATAA
1 AATATAT-AAT-ATATAA
*
373895 ATTAT-TAATATATTAA
1 AATATATAATATA-TAA
* *
373911 AATATATAATATTTTA
1 AATATATAATATATAA
373927 AATA-A-AATTATATAA
1 AATATATAA-TATATAA
373942 AATATATAA-ATATAA
1 AATATATAATATATAA
373957 AATA
1 AATA
373961 AAAACATTCA
Statistics
Matches: 90, Mismatches: 10, Indels: 30
0.69 0.08 0.23
Matches are distributed among these distances:
14 6 0.07
15 29 0.32
16 33 0.37
17 21 0.23
18 1 0.01
ACGTcount: A:0.60, C:0.01, G:0.00, T:0.39
Consensus pattern (16 bp):
AATATATAATATATAA
Found at i:373954 original size:49 final size:48
Alignment explanation
Indices: 373858--373955 Score: 110
Period size: 49 Copynumber: 2.0 Consensus size: 48
373848 TAATATTAAT
* *
373858 TTAAACATATAAATATATTAAATTTTAAATAATATAAATTATTAATATA
1 TTAAACATATAAATATATTAAA-TTAAAATAATATAAATTATAAATATA
* *
373907 TTAAA-ATATATAATATTTTAAA-TAAAATTATATAAAATATATAAATATA
1 TTAAACATATA-AATATATTAAATTAAAATAATAT-AAAT-TATAAATATA
373956 AAATAAAAAC
Statistics
Matches: 42, Mismatches: 4, Indels: 6
0.81 0.08 0.12
Matches are distributed among these distances:
47 9 0.21
48 9 0.21
49 24 0.57
ACGTcount: A:0.57, C:0.01, G:0.00, T:0.42
Consensus pattern (48 bp):
TTAAACATATAAATATATTAAATTAAAATAATATAAATTATAAATATA
Found at i:375125 original size:14 final size:14
Alignment explanation
Indices: 375106--375135 Score: 51
Period size: 14 Copynumber: 2.1 Consensus size: 14
375096 AGGTACTAAA
375106 TTATTAATATAACC
1 TTATTAATATAACC
*
375120 TTATTAATATACCC
1 TTATTAATATAACC
375134 TT
1 TT
375136 TTATTTTTAT
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
14 15 1.00
ACGTcount: A:0.37, C:0.17, G:0.00, T:0.47
Consensus pattern (14 bp):
TTATTAATATAACC
Found at i:375278 original size:2 final size:2
Alignment explanation
Indices: 375271--375298 Score: 56
Period size: 2 Copynumber: 14.0 Consensus size: 2
375261 GACTAGCAGA
375271 AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT
375299 GTATTTCTTA
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 26 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:377062 original size:2 final size:2
Alignment explanation
Indices: 377055--377093 Score: 78
Period size: 2 Copynumber: 19.5 Consensus size: 2
377045 ACTCACAAGA
377055 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
377094 ACATGATATA
Statistics
Matches: 37, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 37 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:377385 original size:18 final size:18
Alignment explanation
Indices: 377364--377417 Score: 60
Period size: 18 Copynumber: 3.1 Consensus size: 18
377354 AAAAAATTTT
377364 ATTTTAAATTAAAATAAA
1 ATTTTAAATTAAAATAAA
377382 ATTTTTAAA-TAAAATAAA
1 A-TTTTAAATTAAAATAAA
**
377400 AAATT-AATT-AAATAAA
1 ATTTTAAATTAAAATAAA
377416 AT
1 AT
377418 GGGAAGAGAG
Statistics
Matches: 31, Mismatches: 3, Indels: 6
0.77 0.08 0.15
Matches are distributed among these distances:
16 10 0.32
17 3 0.10
18 11 0.35
19 7 0.23
ACGTcount: A:0.63, C:0.00, G:0.00, T:0.37
Consensus pattern (18 bp):
ATTTTAAATTAAAATAAA
Found at i:377387 original size:19 final size:18
Alignment explanation
Indices: 377365--377400 Score: 63
Period size: 18 Copynumber: 1.9 Consensus size: 18
377355 AAAAATTTTA
377365 TTTTAAATTAAAATAAAAT
1 TTTTAAA-TAAAATAAAAT
377384 TTTTAAATAAAATAAAA
1 TTTTAAATAAAATAAAA
377401 AATTAATTAA
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
18 10 0.59
19 7 0.41
ACGTcount: A:0.61, C:0.00, G:0.00, T:0.39
Consensus pattern (18 bp):
TTTTAAATAAAATAAAAT
Found at i:378306 original size:17 final size:17
Alignment explanation
Indices: 378284--378321 Score: 51
Period size: 17 Copynumber: 2.2 Consensus size: 17
378274 ATGAAATCAT
*
378284 TTAAAAATATAATAA-AA
1 TTAAAAAT-TAAAAATAA
378301 TTAAAAATTAAAAATAA
1 TTAAAAATTAAAAATAA
378318 TTAA
1 TTAA
378322 TAAAATAAGT
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
16 5 0.26
17 14 0.74
ACGTcount: A:0.68, C:0.00, G:0.00, T:0.32
Consensus pattern (17 bp):
TTAAAAATTAAAAATAA
Found at i:378576 original size:5 final size:6
Alignment explanation
Indices: 378547--378586 Score: 53
Period size: 6 Copynumber: 6.5 Consensus size: 6
378537 GCATATGATT
* *
378547 TAAAAA TAAAAA TTAAAAC CAAAAA TAAAAA TAAAAA TAA
1 TAAAAA TAAAAA -TAAAAA TAAAAA TAAAAA TAAAAA TAA
378587 CTTGCCATAT
Statistics
Matches: 29, Mismatches: 4, Indels: 2
0.83 0.11 0.06
Matches are distributed among these distances:
6 24 0.83
7 5 0.17
ACGTcount: A:0.78, C:0.05, G:0.00, T:0.17
Consensus pattern (6 bp):
TAAAAA
Found at i:381639 original size:17 final size:18
Alignment explanation
Indices: 381619--381662 Score: 65
Period size: 17 Copynumber: 2.6 Consensus size: 18
381609 ATTTTTATTT
381619 ATATTTAATTATAAAA-A
1 ATATTTAATTATAAAACA
381636 ATATTTAA-TATAAAACA
1 ATATTTAATTATAAAACA
*
381653 ATTTTTAATT
1 ATATTTAATT
381663 TAATTAAATT
Statistics
Matches: 24, Mismatches: 1, Indels: 3
0.86 0.04 0.11
Matches are distributed among these distances:
16 7 0.29
17 16 0.67
18 1 0.04
ACGTcount: A:0.52, C:0.02, G:0.00, T:0.45
Consensus pattern (18 bp):
ATATTTAATTATAAAACA
Found at i:381670 original size:123 final size:127
Alignment explanation
Indices: 381552--381814 Score: 312
Period size: 123 Copynumber: 2.1 Consensus size: 127
381542 TTTAAATTAT
** *
381552 ATTTTAAATAAATATT-T-TATTT-ATTTGTTTTAGTTTAAATAAATTAAAATAATTAAAATTTT
1 ATTTTAAATAAATATTATCTATTTAATTTAATTTAATTTAAATAAATTAAAATAATTAAAATTTT
*
381614 TATTTATATTTAATTATAAAA-A-AT-AT-TTAATATAAAACAA-TTTTTAATTTAATT-A-A
66 TATTTAAATTTAATTATAAAATATATAATATTAATATAAAACAATTTTTTAATTT-ATTAATA
* * * *
381670 ATTTTAAATAAATTTTTCATCTATTTAATTTAATTTAATTTAAATTAATTAAAATAATTTAATTT
1 ATTTTAAATAAA-TATT-ATCTATTTAATTTAATTTAATTTAAATAAATTAAAATAATTAAAATT
* *
381735 TTTATTTAAATTTAATTATAAAATATATAAATATTAATATAAAATAATTTTTTAATTTTTTAATC
64 TTTATTTAAATTTAATTATAAAATATAT-AATATTAATATAAAACAATTTTTTAATTTATTAAT-
381800 AA
127 -A
381802 ATTTTAAATAAAT
1 ATTTTAAATAAAT
381815 CTATAAAAGG
Statistics
Matches: 120, Mismatches: 10, Indels: 17
0.82 0.07 0.12
Matches are distributed among these distances:
118 12 0.10
119 3 0.03
121 1 0.01
122 5 0.04
123 54 0.45
124 1 0.01
125 2 0.02
127 2 0.02
128 15 0.12
129 11 0.09
131 1 0.01
132 13 0.11
ACGTcount: A:0.46, C:0.02, G:0.01, T:0.51
Consensus pattern (127 bp):
ATTTTAAATAAATATTATCTATTTAATTTAATTTAATTTAAATAAATTAAAATAATTAAAATTTT
TATTTAAATTTAATTATAAAATATATAATATTAATATAAAACAATTTTTTAATTTATTAATA
Found at i:381702 original size:5 final size:5
Alignment explanation
Indices: 381692--381751 Score: 56
Period size: 5 Copynumber: 12.6 Consensus size: 5
381682 TTTTTCATCT
* **
381692 ATTTA ATTTA ATTTA ATTTA AATTA A-TTA AAATA ATTTA ATTT- -TTT-
1 ATTTA ATTTA ATTTA ATTTA ATTTA ATTTA ATTTA ATTTA ATTTA ATTTA
381738 ATTTAA ATTTA ATT
1 ATTT-A ATTTA ATT
381752 ATAAAATATA
Statistics
Matches: 47, Mismatches: 4, Indels: 8
0.80 0.07 0.14
Matches are distributed among these distances:
3 3 0.06
4 7 0.15
5 33 0.70
6 4 0.09
ACGTcount: A:0.43, C:0.00, G:0.00, T:0.57
Consensus pattern (5 bp):
ATTTA
Found at i:381765 original size:21 final size:21
Alignment explanation
Indices: 381741--381780 Score: 64
Period size: 21 Copynumber: 1.9 Consensus size: 21
381731 ATTTTTTATT
381741 TAAAT-TTAATTATAAAATATA
1 TAAATATTAA-TATAAAATATA
381762 TAAATATTAATATAAAATA
1 TAAATATTAATATAAAATA
381781 ATTTTTTAAT
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
21 14 0.78
22 4 0.22
ACGTcount: A:0.60, C:0.00, G:0.00, T:0.40
Consensus pattern (21 bp):
TAAATATTAATATAAAATATA
Found at i:381999 original size:8 final size:8
Alignment explanation
Indices: 381978--382007 Score: 51
Period size: 8 Copynumber: 3.6 Consensus size: 8
381968 ATTAATATTA
381978 TATTAATAT
1 TATTAAT-T
381987 TATTAATT
1 TATTAATT
381995 TATTAATT
1 TATTAATT
382003 TATTA
1 TATTA
382008 GTGTAAAATT
Statistics
Matches: 21, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
8 14 0.67
9 7 0.33
ACGTcount: A:0.40, C:0.00, G:0.00, T:0.60
Consensus pattern (8 bp):
TATTAATT
Found at i:384283 original size:14 final size:14
Alignment explanation
Indices: 384250--384283 Score: 52
Period size: 14 Copynumber: 2.4 Consensus size: 14
384240 GATATGTCAT
384250 ACTAATCCCTAATC
1 ACTAATCCCTAATC
384264 -CTTAATCCCTAATC
1 AC-TAATCCCTAATC
384278 ACTAAT
1 ACTAAT
384284 TCCTCTTAAT
Statistics
Matches: 18, Mismatches: 0, Indels: 4
0.82 0.00 0.18
Matches are distributed among these distances:
13 1 0.06
14 16 0.89
15 1 0.06
ACGTcount: A:0.35, C:0.32, G:0.00, T:0.32
Consensus pattern (14 bp):
ACTAATCCCTAATC
Found at i:387794 original size:27 final size:28
Alignment explanation
Indices: 387728--387832 Score: 90
Period size: 28 Copynumber: 3.8 Consensus size: 28
387718 ATAGAGACGG
* * * *
387728 GGTTGGAGTATCTCCTCAGAATTAATAT
1 GGTTGGAGTATCTCTTCAGAAATAACAA
*
387756 GGTTGGAGTATCTCTTGA-AAATAACAA
1 GGTTGGAGTATCTCTTCAGAAATAACAA
* * **
387783 GGTTGGAGTATCTCTGCA-ATAAAAACGG
1 GGTTGGAGTATCTCTTCAGA-AATAACAA
*
387811 GGTTGGAGTATCCCTTC-GAAAT
1 GGTTGGAGTATCTCTTCAGAAAT
387833 TGATGGGGTT
Statistics
Matches: 62, Mismatches: 13, Indels: 5
0.77 0.16 0.06
Matches are distributed among these distances:
27 25 0.40
28 37 0.60
ACGTcount: A:0.30, C:0.14, G:0.25, T:0.30
Consensus pattern (28 bp):
GGTTGGAGTATCTCTTCAGAAATAACAA
Found at i:387898 original size:79 final size:78
Alignment explanation
Indices: 387800--387999 Score: 222
Period size: 79 Copynumber: 2.6 Consensus size: 78
387790 GTATCTCTGC
* * *
387800 AATAAAAACGGGGTTGGAGTATCC-CTTCGAAATTGATGGGGTTAGAATATCTCCGACATAAAAA
1 AATAAAAATGGGGTTGGAGTATCCTC-TCGAAATTAATGGGGTTAGAATATCTCCAACATAAAAA
* *
387864 ATTTAGTATTTTTGA
65 ATCTA-TATTTTAGA
* * * * * * * * *
387879 AATAAAAATGAGGTTGGAGTATCCTCTCAAAAATAACGAGGTTAGAGTATTTCCAAGATGAAAAA
1 AATAAAAATGGGGTTGGAGTATCCTCTCGAAATTAATGGGGTTAGAATATCTCCAACATAAAAAA
387944 TCTATATTTTAGA
66 TCTATATTTTAGA
* * *
387957 AGTAAAAATGGGGTTGGAGAATCCTCTCGGAATTAATGGGGTT
1 AATAAAAATGGGGTTGGAGTATCCTCTCGAAATTAATGGGGTT
388000 GGAGTATCCT
Statistics
Matches: 98, Mismatches: 22, Indels: 3
0.80 0.18 0.02
Matches are distributed among these distances:
78 43 0.44
79 54 0.55
80 1 0.01
ACGTcount: A:0.37, C:0.10, G:0.23, T:0.30
Consensus pattern (78 bp):
AATAAAAATGGGGTTGGAGTATCCTCTCGAAATTAATGGGGTTAGAATATCTCCAACATAAAAAA
TCTATATTTTAGA
Found at i:388005 original size:78 final size:77
Alignment explanation
Indices: 387800--388031 Score: 234
Period size: 78 Copynumber: 3.0 Consensus size: 77
387790 GTATCTCTGC
* * * * *
387800 AATAAAAACGGGGTTGGAGTATCC-CTTCGAAATTGATGGGGTTAGAATATCTCCGACATAAAAA
1 AATAAAAATGGGGTTGGAGTATCCTC-TCGAAATTAATGGGGTTAGAGTAT-TCCGAGATGAAAA
* *
387864 ATTTAGTATTTTTGA
64 ATCTA-TATTTTAGA
* * * * * *
387879 AATAAAAATGAGGTTGGAGTATCCTCTCAAAAATAACGAGGTTAGAGTATTTCCAAGATGAAAAA
1 AATAAAAATGGGGTTGGAGTATCCTCTCGAAATTAATGGGGTTAGAGTA-TTCCGAGATGAAAAA
387944 TCTATATTTTAGA
65 TCTATATTTTAGA
* * * *
387957 AGTAAAAATGGGGTTGGAGAATCCTCTCGGAATTAATGGGGTTGGAGTA-TCCTTGAGATGAAAA
1 AATAAAAATGGGGTTGGAGTATCCTCTCGAAATTAATGGGGTTAGAGTATTCC--GAGATGAAAA
*
388021 ATCGATATTTT
64 ATCTATATTTT
388032 TGGAAGAAAA
Statistics
Matches: 125, Mismatches: 24, Indels: 9
0.79 0.15 0.06
Matches are distributed among these distances:
76 3 0.02
78 67 0.54
79 53 0.42
80 2 0.02
ACGTcount: A:0.37, C:0.10, G:0.22, T:0.31
Consensus pattern (77 bp):
AATAAAAATGGGGTTGGAGTATCCTCTCGAAATTAATGGGGTTAGAGTATTCCGAGATGAAAAAT
CTATATTTTAGA
Found at i:391045 original size:21 final size:21
Alignment explanation
Indices: 391019--391063 Score: 63
Period size: 21 Copynumber: 2.1 Consensus size: 21
391009 GTATTAGTAT
*
391019 ATCCACTGAATATATCGATAC
1 ATCCACTAAATATATCGATAC
* *
391040 ATCCACTAAATGTATTGATAC
1 ATCCACTAAATATATCGATAC
391061 ATC
1 ATC
391064 TGATCATGGA
Statistics
Matches: 21, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
21 21 1.00
ACGTcount: A:0.38, C:0.22, G:0.09, T:0.31
Consensus pattern (21 bp):
ATCCACTAAATATATCGATAC
Found at i:397282 original size:76 final size:77
Alignment explanation
Indices: 397039--397488 Score: 290
Period size: 78 Copynumber: 5.8 Consensus size: 77
397029 TGAGAAATCT
* * ** * * * * *
397039 AAGTCTCTAAGGTCATGTGAGAACTTTCATGCCAATGCATGTTCATTAGGGTTATTTTGGTAATA
1 AAGTCTCTAGGGTTATGTG-GAACTTTCATGTAAATACATGTCCATTAAGGTCATTTAGGTAATA
397104 TTAAATTAATATC
65 TTAAATTAATATC
* * * * * * *
397117 GAGTCTCTAGGATTATGTGAGGACTTTTATGTCAATATATGTCTATTAAGGTCATTTAGGTAATA
1 AAGTCTCTAGGGTTATGTG-GAACTTTCATGTAAATACATGTCCATTAAGGTCATTTAGGTAATA
* *
397182 CTATATTAATATC
65 TTAAATTAATATC
* * *
397195 GAA-TCTTTAGGGTTATGTGGACACTTTCGTGTAAATACGTGTCCATT-A-GTCATTTAGGTAAT
1 -AAGTCTCTAGGGTTATGTGGA-ACTTTCATGTAAATACATGTCCATTAAGGTCATTTAGGTAAT
*
397257 ATTACATTAATAGT-
64 ATTAAATTAATA-TC
* * *** * * * *
397271 AAGTCTCTAGGGTTATGTTGGAACTTTTATATTGGTACATGTCTATTAGGGTTCA-TTAAGTGAT
1 AAGTCTCTAGGGTTATG-TGGAACTTTCATGTAAATACATGTCCATTAAGG-TCATTTAGGTAAT
397335 ATTAAATTAATATC
64 ATTAAATTAATATC
* * * * * * * * **
397349 AAG--T-TAAGGTCATGTGGAAACTTTCATATTAATACATTTCTAGTAAGGTTATTTAAATAATA
1 AAGTCTCTAGGGTTATGTGG-AACTTTCATGTAAATACATGTCCATTAAGGTCATTTAGGTAATA
*
397411 TT--GTTCAAATATC
65 TTAAATT--AATATC
* * * * ** *
397424 GAGTCTCTATGGTCATGTGAGAACTTTCATATCGATACATGTCCATTAAGGTTATTTAGGTAATA
1 AAGTCTCTAGGGTTATGTG-GAACTTTCATGTAAATACATGTCCATTAAGGTCATTTAGGTAATA
397489 GTGTATCAAA
Statistics
Matches: 293, Mismatches: 62, Indels: 34
0.75 0.16 0.09
Matches are distributed among these distances:
73 2 0.01
74 5 0.02
75 52 0.18
76 55 0.19
77 9 0.03
78 165 0.56
79 5 0.02
ACGTcount: A:0.31, C:0.11, G:0.18, T:0.40
Consensus pattern (77 bp):
AAGTCTCTAGGGTTATGTGGAACTTTCATGTAAATACATGTCCATTAAGGTCATTTAGGTAATAT
TAAATTAATATC
Found at i:397506 original size:78 final size:78
Alignment explanation
Indices: 397356--397506 Score: 189
Period size: 78 Copynumber: 1.9 Consensus size: 78
397346 ATCAAGTTAA
* * * *
397356 GGTCATGTGGAAACTTTCATATTAATACATTTCTAGTAAGGTTATTTAAATAATATTGTTCAAAT
1 GGTCATGTGGAAACTTTCATATCAATACATGTCCAGTAAGGTTATTTAAATAATAGTGTTCAAAT
397421 ATCGAGTCTCTAT
66 ATCGAGTCTCTAT
* * **
397434 GGTCATGT-GAGAACTTTCATATCGATACATGTCCATTAAGGTTATTTAGGTAATAGTGTATCAA
1 GGTCATGTGGA-AACTTTCATATCAATACATGTCCAGTAAGGTTATTTAAATAATAGTGT-TCAA
*
397498 A-ATGGAGTC
64 ATATCGAGTC
397507 CTTAGGATTA
Statistics
Matches: 62, Mismatches: 9, Indels: 4
0.83 0.12 0.05
Matches are distributed among these distances:
77 2 0.03
78 55 0.89
79 5 0.08
ACGTcount: A:0.32, C:0.12, G:0.18, T:0.38
Consensus pattern (78 bp):
GGTCATGTGGAAACTTTCATATCAATACATGTCCAGTAAGGTTATTTAAATAATAGTGTTCAAAT
ATCGAGTCTCTAT
Found at i:398298 original size:16 final size:17
Alignment explanation
Indices: 398279--398311 Score: 50
Period size: 18 Copynumber: 1.9 Consensus size: 17
398269 AATATACTTA
398279 ATAA-TAAAATATAATG
1 ATAATTAAAATATAATG
398295 ATAATTTAAAATATAAT
1 ATAA-TTAAAATATAAT
398312 AAATAATAAC
Statistics
Matches: 15, Mismatches: 0, Indels: 2
0.88 0.00 0.12
Matches are distributed among these distances:
16 4 0.27
18 11 0.73
ACGTcount: A:0.61, C:0.00, G:0.03, T:0.36
Consensus pattern (17 bp):
ATAATTAAAATATAATG
Found at i:400513 original size:8 final size:8
Alignment explanation
Indices: 400500--400533 Score: 50
Period size: 8 Copynumber: 4.2 Consensus size: 8
400490 AAAATAATTT
400500 TATTTAAA
1 TATTTAAA
400508 TATTTAAA
1 TATTTAAA
*
400516 TATTTTAA
1 TATTTAAA
*
400524 TTTTTAAA
1 TATTTAAA
400532 TA
1 TA
400534 ATTTTTAATT
Statistics
Matches: 22, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
8 22 1.00
ACGTcount: A:0.44, C:0.00, G:0.00, T:0.56
Consensus pattern (8 bp):
TATTTAAA
Found at i:400529 original size:24 final size:24
Alignment explanation
Indices: 400502--400599 Score: 91
Period size: 22 Copynumber: 4.2 Consensus size: 24
400492 AATAATTTTA
400502 TTTAAATATTTAAATATTTTAATT
1 TTTAAATATTTAAATATTTTAATT
*
400526 TTTAAATAATTTTTAAT-TTTTAATT
1 TTTAAAT-A-TTTAAATATTTTAATT
*
400551 TTTAAA-A-TTAAGATATGTT-ATT
1 TTTAAATATTTAA-ATATTTTAATT
* *
400573 TTTAAAAAATTAAATA--TTAATT
1 TTTAAATATTTAAATATTTTAATT
400595 TTTAA
1 TTTAA
400600 GAAAATATTA
Statistics
Matches: 64, Mismatches: 3, Indels: 16
0.77 0.04 0.19
Matches are distributed among these distances:
21 5 0.08
22 19 0.30
23 8 0.12
24 11 0.17
25 15 0.23
26 6 0.09
ACGTcount: A:0.43, C:0.00, G:0.02, T:0.55
Consensus pattern (24 bp):
TTTAAATATTTAAATATTTTAATT
Found at i:400541 original size:18 final size:16
Alignment explanation
Indices: 400500--400548 Score: 62
Period size: 16 Copynumber: 2.9 Consensus size: 16
400490 AAAATAATTT
* *
400500 TATTTAAATATTTAAA
1 TATTTTAATTTTTAAA
400516 TATTTTAATTTTTAAA
1 TATTTTAATTTTTAAA
400532 TAATTTTTAATTTTTAA
1 T-A-TTTTAATTTTTAA
400549 TTTTTAAAAT
Statistics
Matches: 29, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
16 15 0.52
17 1 0.03
18 13 0.45
ACGTcount: A:0.41, C:0.00, G:0.00, T:0.59
Consensus pattern (16 bp):
TATTTTAATTTTTAAA
Found at i:400680 original size:20 final size:20
Alignment explanation
Indices: 400647--400686 Score: 64
Period size: 20 Copynumber: 2.0 Consensus size: 20
400637 ATAAAGAAAA
400647 AATTAATAAATTTTTTCAAAT
1 AATTAATAAATTTTTT-AAAT
400668 AATTAAT-AATTTTTTAAAT
1 AATTAATAAATTTTTTAAAT
400687 TAAAATAATA
Statistics
Matches: 19, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
19 4 0.21
20 8 0.42
21 7 0.37
ACGTcount: A:0.47, C:0.03, G:0.00, T:0.50
Consensus pattern (20 bp):
AATTAATAAATTTTTTAAAT
Found at i:400693 original size:18 final size:19
Alignment explanation
Indices: 400646--400695 Score: 52
Period size: 20 Copynumber: 2.7 Consensus size: 19
400636 AATAAAGAAA
*
400646 AAATTAATA-AATTTTTTC
1 AAATTAAAATAATTTTTTC
400664 AAA-TAATTAATAATTTTTT-
1 AAATTAA--AATAATTTTTTC
400683 AAATTAAAATAAT
1 AAATTAAAATAAT
400696 AAGATATTTT
Statistics
Matches: 27, Mismatches: 1, Indels: 8
0.75 0.03 0.22
Matches are distributed among these distances:
17 3 0.11
18 9 0.33
19 4 0.15
20 11 0.41
ACGTcount: A:0.52, C:0.02, G:0.00, T:0.46
Consensus pattern (19 bp):
AAATTAAAATAATTTTTTC
Found at i:400695 original size:21 final size:21
Alignment explanation
Indices: 400645--400697 Score: 56
Period size: 21 Copynumber: 2.5 Consensus size: 21
400635 AAATAAAGAA
400645 AAAATTAATAAATTTTTTCAAAT
1 AAAA-TAAT-AATTTTTTCAAAT
*
400668 -AATTAATAATTTTTT-AAATT
1 AAAATAATAATTTTTTCAAA-T
400688 AAAATAATAA
1 AAAATAATAA
400698 GATATTTTAA
Statistics
Matches: 26, Mismatches: 2, Indels: 6
0.76 0.06 0.18
Matches are distributed among these distances:
19 3 0.12
20 9 0.35
21 12 0.46
22 2 0.08
ACGTcount: A:0.55, C:0.02, G:0.00, T:0.43
Consensus pattern (21 bp):
AAAATAATAATTTTTTCAAAT
Found at i:400946 original size:24 final size:24
Alignment explanation
Indices: 400919--400978 Score: 75
Period size: 24 Copynumber: 2.5 Consensus size: 24
400909 TTATGGTTTT
*
400919 AAAATAATTTTTTAATTTTGTTAA
1 AAAATAATTTATTAATTTTGTTAA
* * *
400943 AAAATCATATATTAATTTTTTTAA
1 AAAATAATTTATTAATTTTGTTAA
400967 AAATATAATTTA
1 AAA-ATAATTTA
400979 AAACTTTTTA
Statistics
Matches: 29, Mismatches: 6, Indels: 1
0.81 0.17 0.03
Matches are distributed among these distances:
24 23 0.79
25 6 0.21
ACGTcount: A:0.47, C:0.02, G:0.02, T:0.50
Consensus pattern (24 bp):
AAAATAATTTATTAATTTTGTTAA
Found at i:401044 original size:22 final size:23
Alignment explanation
Indices: 401005--401051 Score: 69
Period size: 22 Copynumber: 2.1 Consensus size: 23
400995 GAATATGATC
401005 TTAAAATATAATTTTAAATATTT
1 TTAAAATATAATTTTAAATATTT
* *
401028 TTAAAATA-ATTTTTAAATTTTT
1 TTAAAATATAATTTTAAATATTT
401050 TT
1 TT
401052 GTGAAAACTC
Statistics
Matches: 22, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
22 14 0.64
23 8 0.36
ACGTcount: A:0.43, C:0.00, G:0.00, T:0.57
Consensus pattern (23 bp):
TTAAAATATAATTTTAAATATTT
Found at i:403272 original size:40 final size:41
Alignment explanation
Indices: 403179--403256 Score: 99
Period size: 40 Copynumber: 2.0 Consensus size: 41
403169 ACTTTGATAA
* *
403179 AAAAAATATTAAAA-TAACCTTAAAAGCTCAGTTTTGACAT
1 AAAAATTACTAAAATTAACCTTAAAAGCTCAGTTTTGACAT
*
403219 AAAAATTAC-AAAATTAACCTTAGAAGCTC-GATTTTGAC
1 AAAAATTACTAAAATTAACCTTAAAAGCTCAG-TTTTGAC
403257 GTACAAATGC
Statistics
Matches: 33, Mismatches: 3, Indels: 4
0.82 0.08 0.10
Matches are distributed among these distances:
39 5 0.15
40 28 0.85
ACGTcount: A:0.47, C:0.14, G:0.09, T:0.29
Consensus pattern (41 bp):
AAAAATTACTAAAATTAACCTTAAAAGCTCAGTTTTGACAT
Found at i:404506 original size:15 final size:15
Alignment explanation
Indices: 404479--404523 Score: 54
Period size: 15 Copynumber: 2.9 Consensus size: 15
404469 AAACTTTCTT
*
404479 TTTTTCTTCTTTTCC
1 TTTTTCTTTTTTTCC
**
404494 TTTTTCTTTTTTTTT
1 TTTTTCTTTTTTTCC
404509 TTTTTACTTTTTTTC
1 TTTTT-CTTTTTTTC
404524 AAAGATGATA
Statistics
Matches: 25, Mismatches: 4, Indels: 1
0.83 0.13 0.03
Matches are distributed among these distances:
15 17 0.68
16 8 0.32
ACGTcount: A:0.02, C:0.16, G:0.00, T:0.82
Consensus pattern (15 bp):
TTTTTCTTTTTTTCC
Found at i:404519 original size:9 final size:8
Alignment explanation
Indices: 404473--404523 Score: 61
Period size: 8 Copynumber: 6.5 Consensus size: 8
404463 AAAAGCAAAC
404473 TTTCTTTT
1 TTTCTTTT
*
404481 TTTCTTCT
1 TTTCTTTT
*
404489 TTTC-CTT
1 TTTCTTTT
404496 TTTCTTTT
1 TTTCTTTT
404504 TTT-TTTT
1 TTTCTTTT
404511 TTTACTTTT
1 TTT-CTTTT
404520 TTTC
1 TTTC
404524 AAAGATGATA
Statistics
Matches: 36, Mismatches: 4, Indels: 6
0.78 0.09 0.13
Matches are distributed among these distances:
7 12 0.33
8 17 0.47
9 7 0.19
ACGTcount: A:0.02, C:0.16, G:0.00, T:0.82
Consensus pattern (8 bp):
TTTCTTTT
Found at i:404521 original size:23 final size:23
Alignment explanation
Indices: 404473--404520 Score: 71
Period size: 22 Copynumber: 2.1 Consensus size: 23
404463 AAAAGCAAAC
404473 TTTCTTTTTTTCTTCTTTTCCTT
1 TTTCTTTTTTTCTTCTTTTCCTT
* *
404496 TTTCTTTTTTT-TTTTTTTACTT
1 TTTCTTTTTTTCTTCTTTTCCTT
404518 TTT
1 TTT
404521 TTCAAAGATG
Statistics
Matches: 23, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
22 12 0.52
23 11 0.48
ACGTcount: A:0.02, C:0.15, G:0.00, T:0.83
Consensus pattern (23 bp):
TTTCTTTTTTTCTTCTTTTCCTT
Found at i:404808 original size:40 final size:40
Alignment explanation
Indices: 404759--404849 Score: 94
Period size: 40 Copynumber: 2.3 Consensus size: 40
404749 AATCTCACTA
* *
404759 GTTGCTAACATATTTAAAAAGTCAAAAATTAAT-TTAATTG
1 GTTGGTAACATATTTAAAAAGTC-AAAATTAATCCTAATTG
* ** * *
404799 GTTGGTAACATGTTTGGAAATTCAAATTTAATCCTAATTG
1 GTTGGTAACATATTTAAAAAGTCAAAATTAATCCTAATTG
*
404839 GTTGGAAACAT
1 GTTGGTAACAT
404850 GGCTGAAAGT
Statistics
Matches: 42, Mismatches: 8, Indels: 2
0.81 0.15 0.04
Matches are distributed among these distances:
39 8 0.19
40 34 0.81
ACGTcount: A:0.38, C:0.09, G:0.15, T:0.37
Consensus pattern (40 bp):
GTTGGTAACATATTTAAAAAGTCAAAATTAATCCTAATTG
Found at i:404868 original size:39 final size:40
Alignment explanation
Indices: 404776--404869 Score: 102
Period size: 40 Copynumber: 2.4 Consensus size: 40
404766 ACATATTTAA
* * * **
404776 AAAGTCAAAAATTAAT-TTAATTGGTTGGTAACATGTTTGG
1 AAAGTC-AAATTTAATCCTAATTGGTTGGAAACATGGCTGG
*
404816 AAATTCAAATTTAATCCTAATTGGTTGGAAACATGGCT-G
1 AAAGTCAAATTTAATCCTAATTGGTTGGAAACATGGCTGG
*
404855 AAAGTCAATTTTAAT
1 AAAGTCAAATTTAAT
404870 TTTCATTTGT
Statistics
Matches: 45, Mismatches: 8, Indels: 3
0.80 0.14 0.05
Matches are distributed among these distances:
39 22 0.49
40 23 0.51
ACGTcount: A:0.38, C:0.09, G:0.17, T:0.36
Consensus pattern (40 bp):
AAAGTCAAATTTAATCCTAATTGGTTGGAAACATGGCTGG
Found at i:404969 original size:15 final size:16
Alignment explanation
Indices: 404949--404995 Score: 57
Period size: 16 Copynumber: 3.1 Consensus size: 16
404939 AAAAAAAGTT
404949 TAAAAATTTT-ATATG
1 TAAAAATTTTCATATG
404964 TAAAAAATTTTCA-AT-
1 T-AAAAATTTTCATATG
404979 T-AAAATTTTCATATG
1 TAAAAATTTTCATATG
404994 TA
1 TA
404996 GAAGTTTAAT
Statistics
Matches: 27, Mismatches: 0, Indels: 9
0.75 0.00 0.25
Matches are distributed among these distances:
13 10 0.37
14 2 0.07
15 3 0.11
16 11 0.41
17 1 0.04
ACGTcount: A:0.47, C:0.04, G:0.04, T:0.45
Consensus pattern (16 bp):
TAAAAATTTTCATATG
Found at i:407071 original size:9 final size:9
Alignment explanation
Indices: 407059--407084 Score: 52
Period size: 9 Copynumber: 2.9 Consensus size: 9
407049 TATTACATAT
407059 ATTTCTATC
1 ATTTCTATC
407068 ATTTCTATC
1 ATTTCTATC
407077 ATTTCTAT
1 ATTTCTAT
407085 AATATGTATT
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
9 17 1.00
ACGTcount: A:0.23, C:0.19, G:0.00, T:0.58
Consensus pattern (9 bp):
ATTTCTATC
Found at i:408545 original size:547 final size:548
Alignment explanation
Indices: 407501--408578 Score: 1649
Period size: 547 Copynumber: 2.0 Consensus size: 548
407491 TTCTAGCCAA
* *
407501 TGTCGCAATGTGGTCCGGATACGAATCCCAACCAAGCCCGACTTAAAAATGACCCGAATTCATAT
1 TGTCGCAACGTGGTCCGGATACGAATCCCAACCAAGCCCGACTTAAAAATGACCCGAAGTCATAT
***
407566 GACTGATGAACCGAATAACTTCTATTATTTTGATGACTCCTATTTTGTAGGCCACATTAAAAGAT
66 GACTGATGAAAAAAATAACTTCTATTATTTTGATGACTCCTATTTTGTAGGCCACATTAAAAGAT
* *
407631 GATGTTTTGTATTTTTTTAGGGAATTAGGTCATCGAGATGAATCGCTCGCTCGGTTTAACCCTAA
131 GATATTTTGTATTTTTTTAGGGAATTAGGTCATCGAGATGAATCGCTCACTCGGTTTAACCCTAA
*
407696 ATGATCATTACGAAATGACTATTTTCTTGGAGCCGTCACCAATCTATTTTGGTCGGATGAGATTG
196 ATGATCATTACGAAATGACTATTTTCTTGGAGCCGTCACCAATCTATTTTGGCCGGATGAGATTG
* * * *
407761 GTCACTCATCGGAACTAATATTTTCGAGATTACGAAACCCTTAAAGTTAATCTCAAGATTTACGA
261 GTCACCCATCGGAACTAACATTTTCGAGATTACGAAACCCCTAAAGTTAATCCCAAGATTTACGA
* * * * * *
407826 GATACTAGAGATCATATTTAAGGGTTCGGGAGTCGGTTACAGCCACAAGTAGGGATCGACCTTCT
326 GATACTAGAGATCATACTTAAAGATTCGGAAGTCGATTACAGCCACAAGTAGGGATCGACCCTCT
* * *
407891 CGTGGTGCCCAAAAATTGGTACCTTATTGATTACTTATTAATTTAAAATTTAATTCTTATTCAAT
391 CGTCGTGCCCAAAAATTGGTACCTTATTGATTACATATTAATTTAAAATTTAATTCTTATCCAAT
**
407956 TTCAACATGTGATATTTAATCATAATTCCTGTAAAGAAATTTATTATGCCGTAGGGGGAAAATAG
456 TTCAACATGTGATATTTAATCATAATTCCCATAAAGAAATTTATTATGCCGTAGGGGGAAAATAG
408021 -GTGTTTCGTAAAAAAATTTTTACCAAGT
521 AG-GTTTCGTAAAAAAATTTTTACCAAGT
* * * * * *
408049 TGTCGCAACGTGGTTCGGATATGAATCCCGACTAAGCCCGAGTTAAAAATGGCCCGAAGTCATAT
1 TGTCGCAACGTGGTCCGGATACGAATCCCAACCAAGCCCGACTTAAAAATGACCCGAAGTCATAT
* * *
408114 GATTGATGAAAAAAATAACTTCTATTATTTTGATGACTCCTATTTTGTAGGTCATATTAAAAGAT
66 GACTGATGAAAAAAATAACTTCTATTATTTTGATGACTCCTATTTTGTAGGCCACATTAAAAGAT
* * * *
408179 GATATTTTTTA-TTTTTTAGGGACTTGGGTCATCGAGATGAATCGCTCACTTGGTTTAACCCTAA
131 GATATTTTGTATTTTTTTAGGGAATTAGGTCATCGAGATGAATCGCTCACTCGGTTTAACCCTAA
* * * *
408243 ATGATCATTACGAAATGACTATTTTTTTGGAGTCGTCACTAATCTATTTTGGCCGGGTGAGATTG
196 ATGATCATTACGAAATGACTATTTTCTTGGAGCCGTCACCAATCTATTTTGGCCGGATGAGATTG
* * * * * *
408308 GTCACCCGTCGGAACTAACATTTTCGAGATTACGAAACCCCTGAAGTTAATCCCGAGGTTTATGG
261 GTCACCCATCGGAACTAACATTTTCGAGATTACGAAACCCCTAAAGTTAATCCCAAGATTTACGA
* *
408373 GATAGC-GGAGATCATACTTAAAGATTCGGAAGTCGATTACAGCCACAAGTAGGGATTGACCCTC
326 GATA-CTAGAGATCATACTTAAAGATTCGGAAGTCGATTACAGCCACAAGTAGGGATCGACCCTC
* *
408437 TCGTCGTGCCCAAAAATTGGTACCTTATTGATTACATATTAATTTAAATTTTAATTCTTATCCGA
390 TCGTCGTGCCCAAAAATTGGTACCTTATTGATTACATATTAATTTAAAATTTAATTCTTATCCAA
* *
408502 TTTCAACATGTGATATTTAATCATAATTCCCATAAATAAATTTATTATGCCGTAGGGGGAAAATC
455 TTTCAACATGTGATATTTAATCATAATTCCCATAAAGAAATTTATTATGCCGTAGGGGGAAAATA
408567 GAGGTTTCGTAA
520 GAGGTTTCGTAA
408579 TTTTTTTTTA
Statistics
Matches: 476, Mismatches: 52, Indels: 5
0.89 0.10 0.01
Matches are distributed among these distances:
547 349 0.73
548 127 0.27
ACGTcount: A:0.31, C:0.17, G:0.19, T:0.33
Consensus pattern (548 bp):
TGTCGCAACGTGGTCCGGATACGAATCCCAACCAAGCCCGACTTAAAAATGACCCGAAGTCATAT
GACTGATGAAAAAAATAACTTCTATTATTTTGATGACTCCTATTTTGTAGGCCACATTAAAAGAT
GATATTTTGTATTTTTTTAGGGAATTAGGTCATCGAGATGAATCGCTCACTCGGTTTAACCCTAA
ATGATCATTACGAAATGACTATTTTCTTGGAGCCGTCACCAATCTATTTTGGCCGGATGAGATTG
GTCACCCATCGGAACTAACATTTTCGAGATTACGAAACCCCTAAAGTTAATCCCAAGATTTACGA
GATACTAGAGATCATACTTAAAGATTCGGAAGTCGATTACAGCCACAAGTAGGGATCGACCCTCT
CGTCGTGCCCAAAAATTGGTACCTTATTGATTACATATTAATTTAAAATTTAATTCTTATCCAAT
TTCAACATGTGATATTTAATCATAATTCCCATAAAGAAATTTATTATGCCGTAGGGGGAAAATAG
AGGTTTCGTAAAAAAATTTTTACCAAGT
Found at i:409538 original size:16 final size:15
Alignment explanation
Indices: 409512--409542 Score: 53
Period size: 16 Copynumber: 2.0 Consensus size: 15
409502 ATGAAAAAGA
409512 ATTTTTTATTATTTT
1 ATTTTTTATTATTTT
409527 ATTTTGTTATTATTTT
1 ATTTT-TTATTATTTT
409543 TTATTTAATT
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
15 5 0.33
16 10 0.67
ACGTcount: A:0.19, C:0.00, G:0.03, T:0.77
Consensus pattern (15 bp):
ATTTTTTATTATTTT
Found at i:411069 original size:17 final size:16
Alignment explanation
Indices: 411021--411071 Score: 68
Period size: 15 Copynumber: 3.2 Consensus size: 16
411011 TGGGAGCTGC
411021 TTGTTGTTTGCTAGAG
1 TTGTTGTTTGCTAGAG
* *
411037 TTGCTG-TTGCTGGAG
1 TTGTTGTTTGCTAGAG
411052 TTCGTTGTTTGCTAGAG
1 TT-GTTGTTTGCTAGAG
411069 TTG
1 TTG
411072 CTCGTGAAAG
Statistics
Matches: 29, Mismatches: 4, Indels: 4
0.78 0.11 0.11
Matches are distributed among these distances:
15 10 0.34
16 9 0.31
17 10 0.34
ACGTcount: A:0.10, C:0.10, G:0.33, T:0.47
Consensus pattern (16 bp):
TTGTTGTTTGCTAGAG
Found at i:411681 original size:138 final size:137
Alignment explanation
Indices: 411281--411705 Score: 637
Period size: 138 Copynumber: 3.1 Consensus size: 137
411271 TAGCCCCCCA
*
411281 CATG-TTGCATGCTTCATGATTTTCTCTATGTGG-CTTCCAATTCATTTTGTTTGCTATATGTTT
1 CATGATTGCATGCTTCATGATTTTCTCCATGTGGCCTT-CAATTCATTTTGTTTGC-ATATGTTT
* *
411344 CTTCATGATTTGCATCTCCTATCACTTTTTCATTTACACGTTTG-TTTGCTTTCTTTCTATTTGC
64 CTTCATGATTTGCATCTCCCATCACTTTTTCATTTACACG-TTGCTTTGCTTTCTTTCCATTTGC
411408 TTATGTTCCT
128 TTATGTTCCT
411418 CATGATTGCATGCTTCATGATTTTC-CCAATGTGGTCAC-T-AATTCATTTTGTTTGCATATGTT
1 CATGATTGCATGCTTCATGATTTTCTCC-ATGTGG-C-CTTCAATTCATTTTGTTTGCATATGTT
* * *
411480 TCTTCATGATTTGCATCTCCCATCATTTTTTCATTTACACATTACTTTGCTTTCTTTCCATTTGC
63 TCTTCATGATTTGCATCTCCCATCACTTTTTCATTTACACGTTGCTTTGCTTTCTTTCCATTTGC
*
411545 TTGTGTTCCT
128 TTATGTTCCT
*
411555 CATGATTGCATGCTTCATGATTGTCTCCATGTGGCCTTCAATTCATTTTGTTTGCAATATGTTTC
1 CATGATTGCATGCTTCATGATTTTCTCCATGTGGCCTTCAATTCATTTTGTTTGC-ATATGTTTC
** * *
411620 TTCATGATTTATATCTCCCATCACTTTTTCATTTGCATGTTGCTTTGCTTTCTTTCCATTTGCTT
65 TTCATGATTTGCATCTCCCATCACTTTTTCATTTACACGTTGCTTTGCTTTCTTTCCATTTGCTT
411685 ATGTTCCT
130 ATGTTCCT
411693 CATGATTGCATGC
1 CATGATTGCATGC
411706 AAGGAATGGC
Statistics
Matches: 262, Mismatches: 16, Indels: 19
0.88 0.05 0.06
Matches are distributed among these distances:
135 1 0.00
136 4 0.02
137 124 0.47
138 131 0.50
140 1 0.00
141 1 0.00
ACGTcount: A:0.16, C:0.21, G:0.13, T:0.50
Consensus pattern (137 bp):
CATGATTGCATGCTTCATGATTTTCTCCATGTGGCCTTCAATTCATTTTGTTTGCATATGTTTCT
TCATGATTTGCATCTCCCATCACTTTTTCATTTACACGTTGCTTTGCTTTCTTTCCATTTGCTTA
TGTTCCT
Found at i:411778 original size:85 final size:85
Alignment explanation
Indices: 411635--411805 Score: 315
Period size: 85 Copynumber: 2.0 Consensus size: 85
411625 GATTTATATC
**
411635 TCCCATCACTTTTTCATTTGCATGTTGCTTTGCTTTCTTTCCATTTGCTTATGTTCCTCATGATT
1 TCCCATCACTTTTTCATTTGCACATTGCTTTGCTTTCTTTCCATTTGCTTATGTTCCTCATGATT
411700 GCATGCAAGGAATGGCAAAA
66 GCATGCAAGGAATGGCAAAA
*
411720 TCCCATCACTTTTTCATTTGCACATTGCTTTGCTTTCTTTCCATTTGCTTGTGTTCCTCATGATT
1 TCCCATCACTTTTTCATTTGCACATTGCTTTGCTTTCTTTCCATTTGCTTATGTTCCTCATGATT
411785 GCATGCAAGGAATGGCAAAA
66 GCATGCAAGGAATGGCAAAA
411805 T
1 T
411806 GCCAACTTGC
Statistics
Matches: 83, Mismatches: 3, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
85 83 1.00
ACGTcount: A:0.20, C:0.23, G:0.15, T:0.42
Consensus pattern (85 bp):
TCCCATCACTTTTTCATTTGCACATTGCTTTGCTTTCTTTCCATTTGCTTATGTTCCTCATGATT
GCATGCAAGGAATGGCAAAA
Found at i:412524 original size:42 final size:42
Alignment explanation
Indices: 412339--413067 Score: 791
Period size: 42 Copynumber: 17.2 Consensus size: 42
412329 TAAATAAGGT
* * * *
412339 AGTCTTCAGGGTCAAAGCCGACAAGCAGACTGAGGGATAGAAA
1 AGTCTCCAGGGTCAAAGCCGACAGGCAGACTAAGGG-TAGGAA
* * *
412382 AGTCTCCAAGGTCAAAGTCGACAGGCAAACTAAGGGATAGGAA
1 AGTCTCCAGGGTCAAAGCCGACAGGCAGACTAAGGG-TAGGAA
* *
412425 AGTCTCCAAGGTCAAAGCCGACAGGCAGACTAAAAAAAGGGAAGGAA
1 AGTCTCCAGGGTCAAAGCCGACAGGCAGACT-----AAGGGTAGGAA
* * * * **
412472 AGTCTTCAGGGTCAAAACCCACAGGCAGACTAAGGGAAAAAA
1 AGTCTCCAGGGTCAAAGCCGACAGGCAGACTAAGGGTAGGAA
* * *
412514 AGTCTCCAGGGTCAAAGCCAACAGACAGACTGAGGGTAGGAA
1 AGTCTCCAGGGTCAAAGCCGACAGGCAGACTAAGGGTAGGAA
* * * *
412556 AGTCTCCAAGGTCAAAGCCGATAGGTAGACTGAGGGTAGGAA
1 AGTCTCCAGGGTCAAAGCCGACAGGCAGACTAAGGGTAGGAA
* *
412598 AGTCTCCAAGGTCAAAGCCGACTA-GCAAACTAAGGGTAGGAA
1 AGTCTCCAGGGTCAAAGCCGAC-AGGCAGACTAAGGGTAGGAA
* * *
412640 AGTCTCCAGGGTTAAAGCCGACAGGCAGACTTAGGGAAGGAA
1 AGTCTCCAGGGTCAAAGCCGACAGGCAGACTAAGGGTAGGAA
* * * * * * ** *
412682 AGTTTTCAAGGTTAAAACCGACAAGCAGACCGAGGGTAGGGA
1 AGTCTCCAGGGTCAAAGCCGACAGGCAGACTAAGGGTAGGAA
*
412724 AGTCTCCAGGGTCAAAGCCGACAGGCAAACTAAGGGTAGGAA
1 AGTCTCCAGGGTCAAAGCCGACAGGCAGACTAAGGGTAGGAA
* * *
412766 AGTCTCAAGAGTCAAAGCCGACAGGCAGACTAAGGGTAGGGA
1 AGTCTCCAGGGTCAAAGCCGACAGGCAGACTAAGGGTAGGAA
* *
412808 AGTCTCCAGGGTCAAAGCCGATAGGCAGACTCAGGG-AGG-A
1 AGTCTCCAGGGTCAAAGCCGACAGGCAGACTAAGGGTAGGAA
* * * *
412848 AGTCTCCAAGGTTAAAGTCGATAGGCAGACTAAGGGATAGGAA
1 AGTCTCCAGGGTCAAAGCCGACAGGCAGACTAAGGG-TAGGAA
* * * * *
412891 AGTTTCCAGGGTCAAAACCGACAGGCAAACTTAGGGAAGG-A
1 AGTCTCCAGGGTCAAAGCCGACAGGCAGACTAAGGGTAGGAA
* * *
412932 AGTTTCCAGGGTCAAAGCTGACAGACAGACTAAGGGTAGGAA
1 AGTCTCCAGGGTCAAAGCCGACAGGCAGACTAAGGGTAGGAA
* *
412974 AGTCTCTAGGGTCAAAGCCGACATGCAGACTAAGGGTAGGAA
1 AGTCTCCAGGGTCAAAGCCGACAGGCAGACTAAGGGTAGGAA
* * * *
413016 AGTCTCTAGGGTCAAAAGCCAACAGGCACACTAAGGGAAGGAA
1 AGTCTCCAGGGTC-AAAGCCGACAGGCAGACTAAGGGTAGGAA
*
413059 AGTTTCCAG
1 AGTCTCCAG
413068 AAGTTTAATG
Statistics
Matches: 579, Mismatches: 95, Indels: 24
0.83 0.14 0.03
Matches are distributed among these distances:
40 33 0.06
41 39 0.07
42 343 0.59
43 127 0.22
47 32 0.06
48 5 0.01
ACGTcount: A:0.37, C:0.19, G:0.30, T:0.14
Consensus pattern (42 bp):
AGTCTCCAGGGTCAAAGCCGACAGGCAGACTAAGGGTAGGAA
Found at i:421317 original size:20 final size:21
Alignment explanation
Indices: 421292--421330 Score: 71
Period size: 20 Copynumber: 1.9 Consensus size: 21
421282 TCCCGTGTAA
421292 ATGTATCGATACA-ATTTTTG
1 ATGTATCGATACATATTTTTG
421312 ATGTATCGATACATATTTT
1 ATGTATCGATACATATTTT
421331 AAAATATAGC
Statistics
Matches: 18, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
20 13 0.72
21 5 0.28
ACGTcount: A:0.31, C:0.10, G:0.13, T:0.46
Consensus pattern (21 bp):
ATGTATCGATACATATTTTTG
Found at i:421389 original size:20 final size:20
Alignment explanation
Indices: 421364--421415 Score: 79
Period size: 19 Copynumber: 2.6 Consensus size: 20
421354 TACAAGCCAA
**
421364 TGTATCGATACAATTTTTGG
1 TGTATCGATACAATACTTGG
421384 TGTATCGATAC-ATACTTGG
1 TGTATCGATACAATACTTGG
421403 TGTATCGATACAA
1 TGTATCGATACAA
421416 GTTTGGCTAC
Statistics
Matches: 29, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
19 17 0.59
20 12 0.41
ACGTcount: A:0.29, C:0.13, G:0.19, T:0.38
Consensus pattern (20 bp):
TGTATCGATACAATACTTGG
Found at i:421421 original size:19 final size:18
Alignment explanation
Indices: 421364--421421 Score: 71
Period size: 19 Copynumber: 3.0 Consensus size: 18
421354 TACAAGCCAA
421364 TGTATCGATACAATTTTTGG
1 TGTATCGATACAA--TTTGG
*
421384 TGTATCGATACATACTTGG
1 TGTATCGATACA-ATTTGG
421403 TGTATCGATACAAGTTTGG
1 TGTATCGATACAA-TTTGG
421422 CTACTGCCAA
Statistics
Matches: 34, Mismatches: 2, Indels: 5
0.83 0.05 0.12
Matches are distributed among these distances:
18 1 0.03
19 20 0.59
20 12 0.35
21 1 0.03
ACGTcount: A:0.26, C:0.12, G:0.22, T:0.40
Consensus pattern (18 bp):
TGTATCGATACAATTTGG
Found at i:423964 original size:13 final size:13
Alignment explanation
Indices: 423946--423984 Score: 69
Period size: 13 Copynumber: 3.0 Consensus size: 13
423936 ATAATCACCC
*
423946 TGTATCGATACAT
1 TGTATCGATACAA
423959 TGTATCGATACAA
1 TGTATCGATACAA
423972 TGTATCGATACAA
1 TGTATCGATACAA
423985 AGAAAAATGT
Statistics
Matches: 25, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
13 25 1.00
ACGTcount: A:0.36, C:0.15, G:0.15, T:0.33
Consensus pattern (13 bp):
TGTATCGATACAA
Found at i:426086 original size:15 final size:15
Alignment explanation
Indices: 426066--426096 Score: 53
Period size: 15 Copynumber: 2.1 Consensus size: 15
426056 ATTTCGTTTG
*
426066 GAGCTTCTTCATTTT
1 GAGCTTCCTCATTTT
426081 GAGCTTCCTCATTTT
1 GAGCTTCCTCATTTT
426096 G
1 G
426097 GACATTTTTA
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 15 1.00
ACGTcount: A:0.13, C:0.23, G:0.16, T:0.48
Consensus pattern (15 bp):
GAGCTTCCTCATTTT
Found at i:427928 original size:21 final size:21
Alignment explanation
Indices: 427899--427943 Score: 56
Period size: 22 Copynumber: 2.1 Consensus size: 21
427889 AAGCTTTTAT
*
427899 TTTTCTTAGCTAA-TTCATTA
1 TTTTCTTAGCCAAGTTCATTA
*
427919 TTTTCATTAGCCAAGTTCTTTA
1 TTTTC-TTAGCCAAGTTCATTA
427941 TTT
1 TTT
427944 CAACTTGTAA
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
20 5 0.24
21 7 0.33
22 9 0.43
ACGTcount: A:0.22, C:0.16, G:0.07, T:0.56
Consensus pattern (21 bp):
TTTTCTTAGCCAAGTTCATTA
Found at i:427943 original size:22 final size:20
Alignment explanation
Indices: 427894--427943 Score: 55
Period size: 21 Copynumber: 2.4 Consensus size: 20
427884 CATGCAAGCT
*
427894 TTTATTTTTCTTAGCTAATTC
1 TTTA-TTTTCTTAGCCAATTC
*
427915 ATTATTTTCATTAGCCAAGTTC
1 TTTATTTTC-TTAGCCAA-TTC
427937 TTTATTT
1 TTTATTT
427944 CAACTTGTAA
Statistics
Matches: 24, Mismatches: 3, Indels: 3
0.80 0.10 0.10
Matches are distributed among these distances:
20 5 0.21
21 10 0.42
22 9 0.38
ACGTcount: A:0.22, C:0.14, G:0.06, T:0.58
Consensus pattern (20 bp):
TTTATTTTCTTAGCCAATTC
Found at i:430165 original size:20 final size:20
Alignment explanation
Indices: 430140--430191 Score: 79
Period size: 19 Copynumber: 2.6 Consensus size: 20
430130 TACAAGCCAA
**
430140 TGTATCGATACAATTTTTGG
1 TGTATCGATACAATACTTGG
430160 TGTATCGATAC-ATACTTGG
1 TGTATCGATACAATACTTGG
430179 TGTATCGATACAA
1 TGTATCGATACAA
430192 GTTTGGCTAC
Statistics
Matches: 29, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
19 17 0.59
20 12 0.41
ACGTcount: A:0.29, C:0.13, G:0.19, T:0.38
Consensus pattern (20 bp):
TGTATCGATACAATACTTGG
Found at i:430197 original size:19 final size:18
Alignment explanation
Indices: 430140--430197 Score: 71
Period size: 19 Copynumber: 3.0 Consensus size: 18
430130 TACAAGCCAA
430140 TGTATCGATACAATTTTTGG
1 TGTATCGATACAA--TTTGG
*
430160 TGTATCGATACATACTTGG
1 TGTATCGATACA-ATTTGG
430179 TGTATCGATACAAGTTTGG
1 TGTATCGATACAA-TTTGG
430198 CTACTGCCAA
Statistics
Matches: 34, Mismatches: 2, Indels: 5
0.83 0.05 0.12
Matches are distributed among these distances:
18 1 0.03
19 20 0.59
20 12 0.35
21 1 0.03
ACGTcount: A:0.26, C:0.12, G:0.22, T:0.40
Consensus pattern (18 bp):
TGTATCGATACAATTTGG
Found at i:433416 original size:32 final size:32
Alignment explanation
Indices: 433370--433445 Score: 125
Period size: 32 Copynumber: 2.4 Consensus size: 32
433360 GCAGTAGCTT
*
433370 TGTAGCGATACATTGTATCAATACAACACTTA
1 TGTATCGATACATTGTATCAATACAACACTTA
* *
433402 TGTATCGATACATTGTTTCGATACAACACTTA
1 TGTATCGATACATTGTATCAATACAACACTTA
433434 TGTATCGATACA
1 TGTATCGATACA
433446 GTTACTGTTT
Statistics
Matches: 41, Mismatches: 3, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
32 41 1.00
ACGTcount: A:0.34, C:0.18, G:0.13, T:0.34
Consensus pattern (32 bp):
TGTATCGATACATTGTATCAATACAACACTTA
Found at i:433443 original size:19 final size:19
Alignment explanation
Indices: 433383--433445 Score: 66
Period size: 19 Copynumber: 3.6 Consensus size: 19
433373 AGCGATACAT
*
433383 TGTATCAATACAACACTTA
1 TGTATCGATACAACACTTA
433402 TGTATCGAT---ACA--T-
1 TGTATCGATACAACACTTA
*
433415 TGTTTCGATACAACACTTA
1 TGTATCGATACAACACTTA
433434 TGTATCGATACA
1 TGTATCGATACA
433446 GTTACTGTTT
Statistics
Matches: 35, Mismatches: 3, Indels: 12
0.70 0.06 0.24
Matches are distributed among these distances:
13 8 0.23
14 1 0.03
16 6 0.17
18 1 0.03
19 19 0.54
ACGTcount: A:0.35, C:0.19, G:0.11, T:0.35
Consensus pattern (19 bp):
TGTATCGATACAACACTTA
Found at i:433529 original size:21 final size:20
Alignment explanation
Indices: 433503--433541 Score: 69
Period size: 21 Copynumber: 1.9 Consensus size: 20
433493 GTTGGGACCT
433503 TGTATCGATACATTCTAGAAA
1 TGTATCGATACATT-TAGAAA
433524 TGTATCGATACATTTAGA
1 TGTATCGATACATTTAGA
433542 CAAAAATGTG
Statistics
Matches: 18, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
20 4 0.22
21 14 0.78
ACGTcount: A:0.36, C:0.13, G:0.15, T:0.36
Consensus pattern (20 bp):
TGTATCGATACATTTAGAAA
Found at i:434425 original size:43 final size:43
Alignment explanation
Indices: 434359--434447 Score: 151
Period size: 43 Copynumber: 2.1 Consensus size: 43
434349 AAAGATGACG
434359 AAGGAGCCAATATGCTGATTCAAGGCCAACAACATTGGACTTA
1 AAGGAGCCAATATGCTGATTCAAGGCCAACAACATTGGACTTA
* * *
434402 AAGGTGCCAATATGCTGATTCAAGGCCAACGATATTGGACTTA
1 AAGGAGCCAATATGCTGATTCAAGGCCAACAACATTGGACTTA
434445 AAG
1 AAG
434448 AAGATGCCAC
Statistics
Matches: 43, Mismatches: 3, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
43 43 1.00
ACGTcount: A:0.36, C:0.19, G:0.22, T:0.22
Consensus pattern (43 bp):
AAGGAGCCAATATGCTGATTCAAGGCCAACAACATTGGACTTA
Found at i:434532 original size:27 final size:27
Alignment explanation
Indices: 434465--434702 Score: 266
Period size: 28 Copynumber: 8.5 Consensus size: 27
434455 CACCAACTTG
**
434465 TGTGGGCTTTTGAAAGGGTTG-CACCAACT
1 TGTGGGC-TTTG-AA-GGTTGCCACTGACT
* *
434494 TGTGTGCTTTTGAAGGTTGCCACTGTCT
1 TGTGGGC-TTTGAAGGTTGCCACTGACT
434522 TGTGGGCTTTGAAGGTTGCCACTGACT
1 TGTGGGCTTTGAAGGTTGCCACTGACT
434549 TGTGGGCTTTGAAGGTTGCCACTGACT
1 TGTGGGCTTTGAAGGTTGCCACTGACT
434576 TGTGGGCTTTGAAAAGG-TGCCACTGACT
1 TGTGGGCTTTG--AAGGTTGCCACTGACT
*
434604 TGTGGGCTTTGAAAAGG-TACCACTGACT
1 TGTGGGCTTTG--AAGGTTGCCACTGACT
* *
434632 TGTGGGCTTCTAAAGGTTACCACTGACT
1 TGTGGGCTT-TGAAGGTTGCCACTGACT
*
434660 TGTGGGCTTTTGAAAAGGGTGCCACTGACT
1 TGTGGGC-TTTG--AAGGTTGCCACTGACT
*
434690 TGTGAGCTTTGAA
1 TGTGGGCTTTGAA
434703 AAGGTGAGAA
Statistics
Matches: 189, Mismatches: 12, Indels: 18
0.86 0.05 0.08
Matches are distributed among these distances:
27 68 0.36
28 79 0.42
29 22 0.12
30 20 0.11
ACGTcount: A:0.19, C:0.18, G:0.31, T:0.33
Consensus pattern (27 bp):
TGTGGGCTTTGAAGGTTGCCACTGACT
Found at i:436151 original size:1 final size:1
Alignment explanation
Indices: 436147--436198 Score: 50
Period size: 1 Copynumber: 52.0 Consensus size: 1
436137 TTTGTTGTTG
* * * * * *
436147 TTTTTTTGTTTGTTTTTTTTTGTTTTGTTTTGTTTTTTTTTCTTTTTTTTTT
1 TTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTT
436199 GCGGCGGACG
Statistics
Matches: 39, Mismatches: 12, Indels: 0
0.76 0.24 0.00
Matches are distributed among these distances:
1 39 1.00
ACGTcount: A:0.00, C:0.02, G:0.10, T:0.88
Consensus pattern (1 bp):
T
Found at i:436168 original size:10 final size:10
Alignment explanation
Indices: 436148--436197 Score: 73
Period size: 10 Copynumber: 4.9 Consensus size: 10
436138 TTGTTGTTGT
436148 TTTTTTGTTTG
1 TTTTTT-TTTG
436159 TTTTTTTTTG
1 TTTTTTTTTG
*
436169 TTTTGTTTTG
1 TTTTTTTTTG
*
436179 TTTTTTTTTC
1 TTTTTTTTTG
436189 TTTTTTTTT
1 TTTTTTTTT
436198 TGCGGCGGAC
Statistics
Matches: 36, Mismatches: 3, Indels: 1
0.90 0.08 0.03
Matches are distributed among these distances:
10 30 0.83
11 6 0.17
ACGTcount: A:0.00, C:0.02, G:0.10, T:0.88
Consensus pattern (10 bp):
TTTTTTTTTG
Found at i:436186 original size:14 final size:14
Alignment explanation
Indices: 436135--436196 Score: 65
Period size: 14 Copynumber: 4.4 Consensus size: 14
436125 ATCCGGACCC
436135 TTTTTGTTGTTG-TT
1 TTTTTGTT-TTGTTT
436149 TTTTTG-TTTGTTTT
1 TTTTTGTTTTG-TTT
436163 TTTTTGTTTTGTTT
1 TTTTTGTTTTGTTT
* *
436177 TGTTTTTTTTTCTTT
1 T-TTTTGTTTTGTTT
436192 TTTTT
1 TTTTT
436197 TTGCGGCGGA
Statistics
Matches: 42, Mismatches: 2, Indels: 8
0.81 0.04 0.15
Matches are distributed among these distances:
12 3 0.07
13 1 0.02
14 22 0.52
15 16 0.38
ACGTcount: A:0.00, C:0.02, G:0.13, T:0.85
Consensus pattern (14 bp):
TTTTTGTTTTGTTT
Found at i:436197 original size:15 final size:15
Alignment explanation
Indices: 436135--436198 Score: 74
Period size: 15 Copynumber: 4.3 Consensus size: 15
436125 ATCCGGACCC
* *
436135 TTTTTGTTGTTGTTT
1 TTTTTTTTGTTTTTT
*
436150 TTTTGTTTGTTTTTT
1 TTTTTTTTGTTTTTT
* *
436165 TTTGTTTTGTTTTGT
1 TTTTTTTTGTTTTTT
*
436180 TTTTTTTTCTTTTTT
1 TTTTTTTTGTTTTTT
436195 TTTT
1 TTTT
436199 GCGGCGGACG
Statistics
Matches: 40, Mismatches: 9, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
15 40 1.00
ACGTcount: A:0.00, C:0.02, G:0.12, T:0.86
Consensus pattern (15 bp):
TTTTTTTTGTTTTTT
Found at i:450135 original size:19 final size:21
Alignment explanation
Indices: 450111--450162 Score: 63
Period size: 19 Copynumber: 2.6 Consensus size: 21
450101 AGTGATACAT
450111 TGTATCGATACAG-CACT-TA
1 TGTATCGATACAGTCACTGTA
* * *
450130 TGTATCGATAGAGTTACTGTT
1 TGTATCGATACAGTCACTGTA
450151 TGTATCGATACA
1 TGTATCGATACA
450163 AATTGTTGAA
Statistics
Matches: 27, Mismatches: 4, Indels: 2
0.82 0.12 0.06
Matches are distributed among these distances:
19 12 0.44
20 3 0.11
21 12 0.44
ACGTcount: A:0.29, C:0.15, G:0.19, T:0.37
Consensus pattern (21 bp):
TGTATCGATACAGTCACTGTA
Found at i:455511 original size:545 final size:549
Alignment explanation
Indices: 454447--455538 Score: 1723
Period size: 545 Copynumber: 2.0 Consensus size: 549
454437 TGGAGTCGCT
454447 AAGCTATCACAACGTGGTCCGGATATGAATCCCGACCAAGCTCGACTTAAAAATGGCCCGAATTC
1 AAGCTATCACAACGTGGTCCGGATATGAATCCCGACCAAGCTCGACTTAAAAATGGCCCGAATTC
*
454512 ATATGATTGATGAAACAAATAACTTCTATTATTTTGATGACTCCTATTTTGTAGGCCACATTAAA
66 ATATGATTGATGAAACAAATAACTTCTATTATTTTGA-GACTCCTAGTTTGTAGGCCACATTAAA
* * *
454577 AGATGATGTTTTATATTTTTTAGGGACTTAGGTTCATCAAGATGAATCGCTCGCTCGATTAAACC
130 AGATAATGTTTCACATTTTTTAGGGACTTAGGTTCATCAAGATGAATCGCTCGCTCGATTAAACC
* * *
454642 CTAAATGATCATTTCAAAATGACTATTTTCTTGGAGTCGCCACCAATCTATTTTGGTCGAGTGAG
195 CTAAATGATCATTACAAAATGACTATTTTCTTAGAGTCGCCACCAATCTATTTTGGCCGAGTGAG
* *
454707 ATTGGTCACCCGTCAGAACTAACATTTTCGAGATTATGAAACCCCTGAAGTTAATCTCGAGGTTT
260 ATTGGTCACCCATCAGAACTAACATTTTCGAGATTACGAAACCCCTGAAGTTAATCTCGAGGTTT
* * * *
454772 ACGAGATACCAGAGATCATATTTAAGAGTTCAAGATTTGGTTACAGCCACAAGTAGGGATCGATC
325 ACGAGATACCAGAGATCATATTTAAGAGTTCAAGAGTCGATTACAGCCACAAGTAGGGATCGACC
*
454837 CTCTCGTGGTGCCCAAAAATTGGTACCTTATTGATTACATATTAATTTAAATTTTAATTCTTATC
390 CTCTCGTGGTGCCCAAAAATTGGTACCTTATTGATTACATATTAATTTAAATTTAAATTCTTATC
*
454902 CGATTTCAACATGTGATATTTCATCATAATTCCCATAAAGAAATTTATAATGTCATAGGGGG-AA
455 CGATTTCAACATGTGATATTTAATCATAATTCCCATAAAGAAATTTATAATGTCATAGGGGGAAA
*
454966 AATCGAGGTTTCATAAAA-ATATTTTTGCC
520 AATCAAGGTTTCATAAAATATATTTTTGCC
* * *
454995 AAGCTGTCGCAACGTGGTCCGGATATGAATCTCGACCAAGGC-CGACTTAAAAATGGCCCGAATT
1 AAGCTATCACAACGTGGTCCGGATATGAATCCCGACCAA-GCTCGACTTAAAAATGGCCCGAATT
455059 CATATGATTGATGAAACAAATAACTTCTATTATTTTG-GACTCCTAGTTTGTAGGCCACATTAAA
65 CATATGATTGATGAAACAAATAACTTCTATTATTTTGAGACTCCTAGTTTGTAGGCCACATTAAA
* * *
455123 AGATAATGTTTCGCATTTTTTAGGGACTT-GAG-TCATCGAGATGAATCGCTCGCTCGATTTAAC
130 AGATAATGTTTCACATTTTTTAGGGACTTAG-GTTCATCAAGATGAATCGCTCGCTCGATTAAAC
* * * *
455186 CCTAAATGGTCATTACGAAATGACTATTTTCTTAGAGTTGCCACCAATCTATTTTGGCCGGGTGA
194 CCTAAATGATCATTACAAAATGACTATTTTCTTAGAGTCGCCACCAATCTATTTTGGCCGAGTGA
* *
455251 GATTTGTCACCCATCGGAACTAACATTTTCGAGATTACGAAACCCCTGAAGTTAATCTCGAGGTT
259 GATTGGTCACCCATCAGAACTAACATTTTCGAGATTACGAAACCCCTGAAGTTAATCTCGAGGTT
* *
455316 TAC-AGGATACCAGAGATCATATTTAAGAGTTCGAGAGTCGATTATAGCCACAAGTAGGGATCGA
324 TACGA-GATACCAGAGATCATATTTAAGAGTTCAAGAGTCGATTACAGCCACAAGTAGGGATCGA
* * *
455380 CCCTCTCGTGGTGCTCAAAAATTGGTACCTTATTGATTACTGTATTAATTTAAATTTAAATTTTT
388 CCCTCTCGTGGTGCCCAAAAATTGGTACCTTATTGATTAC-ATATTAATTTAAATTTAAATTCTT
** * * *
455445 ATTTGATTTCAACATGTGATATTTAATCGTAATTCCCATAAAGAAATTTATTATGTCGTA-GGGG
452 ATCCGATTTCAACATGTGATATTTAATCATAATTCCCATAAAGAAATTTATAATGTCATAGGGGG
* *
455509 AAAAATCAAGGTTTCGTAAAATTTATTTTT
517 AAAAATCAAGGTTTCATAAAATATATTTTT
455539 TAAAACAAAA
Statistics
Matches: 498, Mismatches: 40, Indels: 13
0.90 0.07 0.02
Matches are distributed among these distances:
544 1 0.00
545 248 0.50
546 145 0.29
547 7 0.01
548 95 0.19
549 2 0.00
ACGTcount: A:0.31, C:0.18, G:0.18, T:0.33
Consensus pattern (549 bp):
AAGCTATCACAACGTGGTCCGGATATGAATCCCGACCAAGCTCGACTTAAAAATGGCCCGAATTC
ATATGATTGATGAAACAAATAACTTCTATTATTTTGAGACTCCTAGTTTGTAGGCCACATTAAAA
GATAATGTTTCACATTTTTTAGGGACTTAGGTTCATCAAGATGAATCGCTCGCTCGATTAAACCC
TAAATGATCATTACAAAATGACTATTTTCTTAGAGTCGCCACCAATCTATTTTGGCCGAGTGAGA
TTGGTCACCCATCAGAACTAACATTTTCGAGATTACGAAACCCCTGAAGTTAATCTCGAGGTTTA
CGAGATACCAGAGATCATATTTAAGAGTTCAAGAGTCGATTACAGCCACAAGTAGGGATCGACCC
TCTCGTGGTGCCCAAAAATTGGTACCTTATTGATTACATATTAATTTAAATTTAAATTCTTATCC
GATTTCAACATGTGATATTTAATCATAATTCCCATAAAGAAATTTATAATGTCATAGGGGGAAAA
ATCAAGGTTTCATAAAATATATTTTTGCC
Found at i:458481 original size:13 final size:13
Alignment explanation
Indices: 458449--458484 Score: 54
Period size: 13 Copynumber: 2.8 Consensus size: 13
458439 ATGAAAAAGA
458449 ATTTTTTATTATT
1 ATTTTTTATTATT
* *
458462 ATATTTTGTTATT
1 ATTTTTTATTATT
458475 ATTTTTTATT
1 ATTTTTTATT
458485 TTTTATTTAA
Statistics
Matches: 19, Mismatches: 4, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
13 19 1.00
ACGTcount: A:0.22, C:0.00, G:0.03, T:0.75
Consensus pattern (13 bp):
ATTTTTTATTATT
Found at i:460392 original size:138 final size:138
Alignment explanation
Indices: 460232--460656 Score: 708
Period size: 138 Copynumber: 3.1 Consensus size: 138
460222 CAGCTCCCCA
*
460232 CATG-TTGCATGCTTCATGATTTTCTCCATGTGGCCTCCAATTCATTTTGTTTGCCAAATGTTTC
1 CATGATTGCATGCTTCATGATTTTCTCCATGTGGCCTCCAATTCATTTTGTTTGCCATATGTTTC
* *
460296 TTCATGATTTGCATTTCCCATCACTTTTTCATTTGCACGTTGCTTTGCTTTCTTTCCATTTACTT
66 TTCATGATTTGCATCTCCCATCACTTTTTCATTTGCACGTTGCTTTGCTTTCTTTCCATTTGCTT
460361 GTGTTCCT
131 GTGTTCCT
* * * *
460369 TATGATTGCATGCTTTATGATTTTCCCCATGTGGTCTCCAATTCATTTTGTTTGCCATATGTTTC
1 CATGATTGCATGCTTCATGATTTTCTCCATGTGGCCTCCAATTCATTTTGTTTGCCATATGTTTC
* * *
460434 TTGATGATTTGCATCTCCCATTACTTTTTCATTTACACGTTGCTTTGCTTTCTTTCCATTTGCTT
66 TTCATGATTTGCATCTCCCATCACTTTTTCATTTGCACGTTGCTTTGCTTTCTTTCCATTTGCTT
460499 GTGTTCCT
131 GTGTTCCT
*
460507 CATTATTGCATGCTTCATGATTTTCTCCATGTGGCCTCCAATTCATTTTGTTTGCCATATGTTTC
1 CATGATTGCATGCTTCATGATTTTCTCCATGTGGCCTCCAATTCATTTTGTTTGCCATATGTTTC
** *
460572 TTCATGATTTGCATCTCCCATCACTTTTTCATTTGCATTTTGCTTTGATTTCTTTCCATTTGCTT
66 TTCATGATTTGCATCTCCCATCACTTTTTCATTTGCACGTTGCTTTGCTTTCTTTCCATTTGCTT
*
460637 TTGTTCCT
131 GTGTTCCT
460645 CATGATTGCATG
1 CATGATTGCATG
460657 GTACATTGCA
Statistics
Matches: 264, Mismatches: 23, Indels: 1
0.92 0.08 0.00
Matches are distributed among these distances:
137 3 0.01
138 261 0.99
ACGTcount: A:0.15, C:0.23, G:0.13, T:0.49
Consensus pattern (138 bp):
CATGATTGCATGCTTCATGATTTTCTCCATGTGGCCTCCAATTCATTTTGTTTGCCATATGTTTC
TTCATGATTTGCATCTCCCATCACTTTTTCATTTGCACGTTGCTTTGCTTTCTTTCCATTTGCTT
GTGTTCCT
Found at i:464098 original size:34 final size:34
Alignment explanation
Indices: 464055--464119 Score: 103
Period size: 34 Copynumber: 1.9 Consensus size: 34
464045 TATTCACATT
* * *
464055 TTTCGAATTCTAATAAAAAATTTATACATTAATC
1 TTTCAAATTCCAATAAAAAATTCATACATTAATC
464089 TTTCAAATTCCAATAAAAAATTCATACATTA
1 TTTCAAATTCCAATAAAAAATTCATACATTA
464120 GAAATATCTT
Statistics
Matches: 28, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
34 28 1.00
ACGTcount: A:0.46, C:0.14, G:0.02, T:0.38
Consensus pattern (34 bp):
TTTCAAATTCCAATAAAAAATTCATACATTAATC
Found at i:469457 original size:34 final size:34
Alignment explanation
Indices: 469414--469482 Score: 138
Period size: 34 Copynumber: 2.0 Consensus size: 34
469404 ACGGTGTTGG
469414 ACAAAGTCCATTTAAATGGTTATGTAATTTTATA
1 ACAAAGTCCATTTAAATGGTTATGTAATTTTATA
469448 ACAAAGTCCATTTAAATGGTTATGTAATTTTATA
1 ACAAAGTCCATTTAAATGGTTATGTAATTTTATA
469482 A
1 A
469483 AATATAGTAT
Statistics
Matches: 35, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
34 35 1.00
ACGTcount: A:0.39, C:0.09, G:0.12, T:0.41
Consensus pattern (34 bp):
ACAAAGTCCATTTAAATGGTTATGTAATTTTATA
Found at i:469498 original size:34 final size:33
Alignment explanation
Indices: 469416--469498 Score: 96
Period size: 34 Copynumber: 2.4 Consensus size: 33
469406 GGTGTTGGAC
* *
469416 AAAGTCCATTTAAATGGTTATGTAATTTTATAAC
1 AAAGT-CATGTAAATGGTTATGTAATTTTATAAA
*
469450 AAAGTCCATTTAAATGGTTATGTAATTTTATAAA
1 AAAGT-CATGTAAATGGTTATGTAATTTTATAAA
469484 ATATAGT-ATGTAAAT
1 A-A-AGTCATGTAAAT
469499 TCATATTTTG
Statistics
Matches: 45, Mismatches: 2, Indels: 4
0.88 0.04 0.08
Matches are distributed among these distances:
34 41 0.91
35 1 0.02
36 3 0.07
ACGTcount: A:0.41, C:0.06, G:0.12, T:0.41
Consensus pattern (33 bp):
AAAGTCATGTAAATGGTTATGTAATTTTATAAA
Found at i:482398 original size:46 final size:44
Alignment explanation
Indices: 482311--482402 Score: 107
Period size: 46 Copynumber: 2.0 Consensus size: 44
482301 TATTATTAAT
* *
482311 TTAATAAATTTTTATTTAATTTTAATTATTAAAATATATAAAATA
1 TTAATAAATTTTTATTTAATATTAATTA-TAAAATAAATAAAATA
482356 TTAATATAACTTTTT-TTTAATATTAATTA-AATAATAAAATAAAATA
1 TTAATA-AA-TTTTTATTTAATATTAATTATAA-AAT-AAATAAAATA
482402 T
1 T
482403 AAAAACTGAT
Statistics
Matches: 41, Mismatches: 2, Indels: 7
0.82 0.04 0.14
Matches are distributed among these distances:
44 2 0.05
45 9 0.22
46 25 0.61
47 5 0.12
ACGTcount: A:0.50, C:0.01, G:0.00, T:0.49
Consensus pattern (44 bp):
TTAATAAATTTTTATTTAATATTAATTATAAAATAAATAAAATA
Done.